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 South Africa and the rest of 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 head the advise of the World Health Organization (WHO), the South African Department of Health (SA DoH) or the advise laid down by you’re the African Centre for Disease Control and Prevention.

This report will be updated every day to keep track with the increasing numbers of cases. Please visit the site regularly for continued updates.

Short epidemic update

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 linked to an Italian national who had travel to 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, a total of 780 laboratory-confirmed cases have been reported in 34 different countries and/or territories. A total of 180 new infections have been recorded on the continent on the 19th of March. The most severely effected countries are: Egypt (n=256), South Africa (n=150), Algeria (n=87), Morocco (n=63) and Senegal (n=31).

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 region on the African continent 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 97 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.

Relatively few infections have been reported in the Central African region to date (n=52). However, the number of infections is rising fast with 18 new infections reported in the last 24 hours.

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, only 32 cases have been reported with 7 cases being reported in the last 24 hours. Most cases are linked to people with a known history of recent travel with no or little to no community transmissions.

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 and to date is one of only four countries in the region, along with Namibia, Zambia and Eswatini, with confirmed cases. Since the 5th of March the number of COVID-19 cases have increased sharply to 156 cases as of the 18th of March 2020, with 35 new infections in the last 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.

South Africa

Currently, a total of 150 cases with 34 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, the Western Cape, and KwaZulu-Natal. 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.

As of the 19th of March 2020, the National Institute for Communicable Diseases (NICD) has conducted 4832 tests for COVID-19. Only 150 of these samples have tested positive for the virus, with 54 new confirmed cases in the last 24 hours. The bulk of infections are concentrated in Gauteng (n=76), the Western Cape (n=46) and KwaZulu-Natal (n=22). The rest of the infections have been reported in Mpumalanga (n=5) and Limpopo (n=1).

For a breakdown of daily incident and cumulative cases please see the plot below:

Sequencing and phylogenetics

Only two 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.

Both 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 hypthesis of transmission via travel between Europe and Nigeria and the DRC respectively.

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.