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World of Genomics: South Africa

Original article written by Poppy-Jayne Morgan, July 2022. Updated by Aleisha Collins, January 2024.

In this instalment of World of Genomics, we explore key aspects of South Africa’s diverse population, the intricacies of its healthcare system and its burgeoning capabilities in the field of genomics.

Still feeling the effects of decades of inequality and under-resourcing, South Africa continues to face significant challenges. With high rates of tuberculosis and HIV, South Africa aims to reduce its disease burden through medical innovations and cutting-edge genomics advancements. As a leader in sequencing the COVID-19 genome, the country is making significant strides at the forefront of genomic research and healthcare.

The population of South Africa

South Africa is the southernmost country in Africa. Its neighbouring countries to the north are Namibia, Botswana and Zimbabwe, to the east are Mozambique and Eswatini and it surrounds the enclaved country of Lesotho. Meanwhile, its southern coast stretches along the South Atlantic and Indian Oceans.

South Africa contains some of the oldest archaeological and human-fossil sites in the world. The Gauteng Province is a UNESCO World Heritage Site and has been branded the ‘Cradle of Humankind’. These findings suggest that various hominid species existed in South Africa from about three million years ago, starting with Australopithecus africanus and modern humans have inhabited South Africa for at least 170,000 years.

During the Iron Age, Bantu-speaking peoples were some of the largest groups. The Dutch colonised South Africa in the 1600s before it became a British colony in the 1800s. South Africa became fully sovereign in 1931.

The country is one of the few in Africa never to have had a coup d’état and regular elections have been held for almost a century. However, the vast majority of black South Africans were not enfranchised until 1994. Apartheid was a system of institutionalised racial oppression that existed in South Africa from 1948 until the early 1990s. This system denied non-white South Africans basic human rights, such as the right to vote. After a long and fraught struggle by anti-apartheid activists, both inside and outside the country, apartheid came to an end, but the economic legacy and social effects of apartheid continue to the present day.

A map of south africa with black text

Description automatically generatedThe country is multilingual with 11 official languages, each of which is guaranteed equal status. Most South Africans are multilingual and able to speak at least two or more of the official languages.

Figure 1 | Map of South Africa (Source: Encyclopaedia Britannica)

Geographic and demographic information

Summary statistics

Land Area: 1,214,470 sq km

Gross domestic product (GDP):

  • Total: USD 405.87 billion (2022)
  • Per capita: USD $6,776.5 (2022)

Population statistics

Population size: 56,978,635 (July 2021 est.)

Infant mortality rate:

  • Total: 26.82 deaths/1,000 live births
  • Male: 29.9 deaths/1,000 live births
  • Female: 23.68 deaths/1,000 live births (2021 est.)

Average life expectancy

  • Total population: 65.04 years
  • Male: 63.68 years
  • Female: 66.42 years (2021 est.).

Ethnicity: In 2018, the ethnicity breakdown of South Africa was Black South African 80.9%, Coloured South African 8.8%, White 7.8% and Indian/Asian 2.5%.

Note: coloured is a term used in South Africa, including on the national census, for persons of mixed-race ancestry who developed a distinct cultural identity over several hundred years.

Healthcare system

When South Africa freed itself of apartheid, the new health care policy emphasised public health care.

In South Africa, private and public health systems exist in parallel. The public system serves most of the population. Authority and service delivery are divided between the National Department of Health, provincial health departments and municipal health departments. South Africa has a critical shortage of medical professionals, with just 0.91 physicians per 1,000 people (2017). All medical training takes place in the public sector but 70% of doctors go into the private sector. 

The public sector uses a Uniform Patient Fee Schedule (UPFS) which categorises the different fees for every type of patient and situation. It groups patients into three categories: full-paying patients, fully subsidised patients (patients who are referred to a hospital by Primary Healthcare Services) and partially subsidised patients (patients whose costs are partially covered based on their income). 

In 2020, the Universal Health Coverage of South Africa was deemed to be 52, in comparison to the global score of 57. In 2021, South Africa’s healthcare system was ranked 56th in the world by health index score.

Universal Health Coverage is a score measured by the World Health Organisation monitoring to what extent all individuals and communities receive the health services they need without suffering financial hardship

As of 2023, South Africa has made progress in its healthcare system, with ongoing efforts to address the country’s healthcare disparities and improve access to medical services. The National Health Insurance (NHI) system has been a major focus of the government’s healthcare reforms. While the specific details of the NHI are still being developed, it aims to create a single National Health Insurance Fund funded by general taxes and contributions from health insurance. The goal is to provide equal access to healthcare for all citizens and reduce disparities among different socio-economic groups.

Health priorities

In South Africa, the most widespread causes of death in 2020 (excluding COVID-related deaths) were tuberculosis, diabetes, cerebrovascular diseases, HIV and hypertensive diseases.

By June 2022, the country had recorded 3.99 million confirmed COVID-19 cases and 101,859 deaths. President Cyril Ramaphosa was recognized as the AU’s ‘COVID-19 champion’ for his diligent efforts in combating the pandemic. Remarkably, the pandemic struck just under a year after the signing of the first Presidential Health Compact which outlined a five-year roadmap towards achieving Universal Health Coverage (UHC) by 2030. The COVID-19 pandemic and subsequent lockdowns significantly disrupted the AU’s public health order and resulted in an economic downturn, diverting resources from public health budgets to tackle the virus.

During the 2nd Presidential Health Summit in Johannesburg in May 2023, President Ramaphosa presented ten key areas for intervention aimed at advancing the introduction of the National Health Insurance (NHI) program. These areas covered human resources, access to medicines and vaccines, infrastructure planning, private sector engagement, quality and safety of primary healthcare, public sector financial management, leadership and governance, community engagement, health information systems and pandemic preparedness.

The NHI is designed to finance a healthcare system that grants South Africans access to quality services based on their needs rather than their socioeconomic status. The program encourages the wealthiest to contribute to the public system and incentivises the utilisation of public health services. Nonetheless, the current healthcare system still grapples with resource distribution challenges. The private health sector accounts for a significant share of health expenditures through out-of-pocket payments and medical schemes, despite only 18% of the population utilizing private healthcare providers. Moreover, about 79% of doctors practice privately, leading to disparities in access to care.

South Africa’s population structure reflects a legacy of continued inequality. While black South Africans are in the majority in every age group, this majority decreases as the age of the population rises. Coloured, Indian and especially white South Africans tend to have longer life expectancies. The population pyramid’s dent at ages 10 to 24 may be a result of the AIDS epidemic in the 1990s and 2000s. About 28.3% of the population are under 15 years old and roughly 9.2% are 60 years or older (2021).  The proportion of elderly individuals is gradually increasing, necessitating prioritised policies and programs to address the needs of this growing demographic.

South Africa has faced extensive healthcare challenges, with HIV/AIDS being a significant obstacle. Despite representing only 0.7% of the global population, the country accounts for 17% of global HIV infections. However, positive strides have been made since 2021, with a substantial number of people living with HIV receiving anti-retroviral therapy. Efforts such as their multi-disease national wellness campaign (2018) and the availability of PrEP have contributed to better management of HIV, leading to a decline of 51% in new infections between 2010 and 2021. Data from March 2023 reveals that 94.2 per cent of South Africans know their HIV status.

Tuberculosis (TB) also remains a significant public health concern in South Africa. The government’s efforts to screen and treat TB are ongoing, with a commitment to screening 90% of those at risk. However, multi-drug-resistant TB remains a challenge, accounting for around 1.8% of new cases. Improving diagnostic techniques, especially for drug-resistant TB cases, remains essential.

South Africa is also increasingly recognizing the importance of addressing chronic diseases, including cancers. The formalisation of National Health Regulations for cancer as a notifiable condition in 2012, has improved the country’s database and capabilities to deal with cancer cases. Competing burdens of disease in South Africa have meant that chronic diseases, particularly cancers, were not perceived as a priority in the country.

Genomic medicine capabilities

South Africa’s Regional Centre of Excellence for Genomic Surveillance and Bioinformatics was established in 2021. From 2021-2022, genomic sequencing activities quadrupled in Southern Africa.

South African labs were the first to detect the Omicron SARS-CoV-2 variant and flagged it to the world. The Network for Genomic Surveillance in South Africa first spotted the mutated variant in sequencing data from Botswana.

The African Pathogen Genomics Initiative has a centre in South Africa. The network has sequenced over 70,000 viral genomes, indicating the country’s rapid progress in scaling up its sequencing capacities to support its public health response and strengthen genomic surveillance.

In February 2021, South Africa halted the Oxford University–AstraZeneca vaccine’s rollout as a result of the vaccine’s disappointing results against the Beta variant of SARS-CoV-2, which was then the main variant in circulation. Without the sequencing capacity, it would not have been possible to identify the major circulating variants of the virus among the population to select a vaccine. Genomic data formed the basis of South Africa’s decision to use Johnson & Johnson and Pfizer COVID-19 vaccines.

Early screening plays a pivotal role in detecting diseases like Cystic Fibrosis (CF) at their initial stages. At present, South Africa has identified less than 600 cases of CF, but experts believe this number represents only a fraction of the actual cases. Regrettably, most infants born with CF in the country go undiagnosed, leading to their premature demise due to CF-related complications and infections during infancy. The lack of awareness about CF among healthcare professionals, the absence of a newborn screening program, geographical challenges in accessing diagnostic services and the similarities between CF’s presentation and more common conditions like TB, HIV and poverty-related malnutrition contribute to the problem. Consequently, many babies with CF in South Africa may not be diagnosed before succumbing to malnutrition-related complications resulting from untreated CF. Consensus guidelines indicate that approximately one in 27 individuals of “Caucasian” ancestry, one in 55 people of mixed-race ancestry and one in 90 individuals of black African ancestry carry the cystic fibrosis gene in South Africa. According to these guidelines, patients who receive two positive sweat-test results should be referred for genetic screening to confirm their diagnosis and identify specific genes involved.

Access to genetic testing within the state setting in South Africa is currently limited but is progressively expanding due to its growing significance. Unfortunately, newborn screening is not a standard hospital practice in the country and remains relatively inaccessible. This lack of policy support has led to a situation where most medical insurers do not cover the costs of screening.

In response to the urgent need, discussions are underway regarding the establishment of a national infant screening program. Notably, in November 2021, the Department of Health published “Clinical Guidelines for Genetics Services,” which recommend newborn screening for congenital disorders where early detection can prevent significant and irreversible morbidity and mortality.

Notable projects

Notable organisations and institutions

Notable individuals

  • Linda-Gail Barker: Barker is CEO of the Desmond Tutu HIV Foundation and former President of the International AIDS Society. In 2009, she won the Royal Society Pfizer Award for her research into tuberculosis epidemiology.
  • Sydney Brenner: Brenner was a biologist who was awarded the Nobel Prize in Physiology or Medicine in 2002 for research into the genetic regulation of organ development and programmed cell death.
  • Sharon Fonn: Fonn is a Professor of Public Health at the University of Witwatersrand. Her work has focused on cervical cancer, health systems and developing African capacity for public health research.
  • Tulio De Oliveira: Oliveira is the Director of the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) in Durban and the Centre for Epidemic Response and Innovation in Stellenbosch. He led the team that confirmed the Beta and Omicron variants of the COVID-19 virus.
  • Michele Ramsay: Ramsay is a Professor of Human Genetics at the National Health Laboratory Service and former President of the African Society of Human Genetics. Her research investigates single-gene disorders, epigenetics and obesity.  
  • Denise Shaw: Shaw is a Professor of Human Genetics at the Institute of Cell and Molecular Science at Queen Mary, University of London. Her fields of expertise include cell and molecular biology, cancer genetics and epigenetics and the molecular pathology of paediatric brain tumours.
  • Max Theiler: Theiler was a virologist who was awarded the Nobel Prize in Physiology or Medicine in 1951 for developing a vaccine against yellow fever. He was the first African-born Nobel laureate.

The future genomics landscape

The current government is working to establish a national health insurance (NHI) system out of concerns for discrepancies within the national healthcare system, such as unequal access to healthcare amongst different socio-economic groups. Although the details and outline of the proposal have yet to be released, the NHI is speculated to propose that there will be a single National Health Insurance Fund for health insurance. This fund is expected to draw its revenue from general taxes and some sort of health insurance contribution. 

The Human Heredity and Health in Africa (H3Africa) Project invests in improving infrastructure and capacity building for genome research in Africa. Several H3Africa bioinformatics nodes are in South Africa. These databases will illuminate studies of human variation worldwide, in part because the great genomic diversity in Africans can uncover links to medical conditions.

The goal and vision for the SAMRC Genomics Centre is to grow South Africa’s capacity for whole human genome sequencing and engage in an Afrocentric approach to reducing South Africa’s burden of disease. Lifestyle diseases such as hypertension, stroke heart disease, diabetes and cancer and infectious diseases, particularly tuberculosis and HIV-AIDS are key priorities.

Currently, South Africans are exposed to medicine that has been developed outside of Africa and researched on a different gene pool. Drug failure and adverse side effects could be curbed by a better understanding of effectiveness in the South African population. A desire to improve the diversity of genomic data and enhance the understanding of priority diseases are key drivers for the future of genomics in South Africa.

In February 2023, the 14th International Congress of Human Genetics was held in Cape, South Africa.

In 2011, the Southern Africa Human Genome Project was launched, however, it only managed to sequence 24 genomes and excluded health data. Last month, the Department of Science and Innovation (DSI) announced that they are considering the launch of a ‘110,000 genomes project’. This would involve randomly selecting 100,000 participants from the South African population and a further 10,000 participants with rare diseases. This is highly significant, as fewer than 3% of genomic research participants are of African descent. As a result, the success of this project could vastly improve the health of South Africa’s population and be at the forefront of genomics research across Africa.

Overall, South Africa remains committed to advancing its genomics capabilities and leveraging this technology to improve healthcare outcomes for its population. However, challenges in healthcare disparities, infectious diseases and chronic conditions persist and the country continues to work towards achieving equitable access to quality healthcare services for all its citizens.


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