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World of Genomics: South Africa

Poppy-Jayne Morgan 19 July 2022

Home to the Springboks, both the antelope and the rugby team, we travel to South Africa for the latest in our World of Genomics series. Still feeling the effects of decades of inequality and under-resourcing, South Africa has some of the highest rates of tuberculosis and HIV in the world and wishes to reduce its disease burden using medical innovations. A leader in sequencing the COVID-19 genome, this nation is stepping to the forefront of genomics.

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 finds 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.

The 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: 1.219 million km2
  • Gross domestic product (GDP):
    • Total: USD$419.95 billion
    • Per capita: USD$6,994.2

Population statistics

  • Population size: In 2021, the total population of South Africa was estimated to be 60,041,996.
  • Birth rate: In 2020, the crude birth rate was 20 per 1,000 people.
  • Death rate: In 2020, the crude death rate was 9 death per 1,000 people.
  • Infant mortality rate: In 2020, the crude infant mortality rate was 26 deaths per 1,000 live births.
  • Average life expectancy: In 2020, the average life expectancy was 64 years.
  • Ethnicity: In 2017, the ethnicity breakdown of South Africa was Black South African 81%, Coloured South African 8%, White 8% and other 2%.

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 the vast majority of the population. Authority and service delivery are divided between the national Department of Health, provincial health departments and municipal health departments.

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. 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. In 2021, South Africa’s healthcare system was ranked 56th in the world by health index score.

South Africa has a critical shortage of medical professionals, with just 1.3 nurses and 0.8 physicians per 1,000 people. All medical training takes place in the public sector but 70% of doctors go into the private sector. 

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.

Tuberculosis (TB) is a significant public health issue in South Africa. It is the leading cause of death and about 89,000 people die from it annually. Effective treatments are available and the country has made progress in fighting the disease, but much more is needed to bring it under control. The government is committed to screening 90% of those at risk of contracting TB. However, around 1.8% of new cases of TB in South Africa are multi-drug resistant. Current diagnostic techniques often miss cases, especially drug resistant TB cases. South Africa was one of the first countries to roll out the WHO-recommended Xpert MTB/RIF assay, which is more successful at identifying drug resistant TB.

The estimated HIV prevalence rate in South Africa is approximately 13.7%, with 8.2 million people living with HIV in 2021. South Africa has been working to create a program to distribute anti-retroviral therapy treatment. In 2018, South Africa reported that 4.5 million people were on life-saving anti-retroviral therapy and has made positive steps in screening for HIV, with 90% of people living with HIV aware of their status. South Africa was the first country in sub-Saharan Africa to fully approve PrEP, which is now being made available to people at high risk of infection.

In 2018, South Africa launched a multi-disease national wellness campaign to accelerate screening and testing for HIV, tuberculosis, sexually transmitted infections and noncommunicable diseases, including hypertension and diabetes.

Competing burdens of disease in South Africa has meant that chronic diseases, and particularly cancers, were not perceived as a priority in the country. Since 2012, the formalisation of new National Health Regulations made cancer a notifiable condition, increasing South Africa’s database and capabilities to deal with cancer.  

South Africa’s population structure holds 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 live longer. In addition, the dent in South Africa’s population pyramid at ages 10 to 24 may be a legacy of South Africa’s AIDS epidemic of the 1990s and 2000s.

About 28.3% of the population are under 15 years old and roughly 9.2% are 60 years or older. The proportion of elderly persons in South Africa is increasing over time and therefore, policies and programs to care for the needs of this growing population will need to be prioritised.

As of June 2022, South Africa had 3.99 million confirmed COVID-19 cases and 101,859 confirmed COVID-19 deaths.

Genomic medicine capabilities

South Africa’s Regional Centre of Excellence for Genomic Surveillance and Bioinformatics was established in 2021. Since then, genomic sequencing activities have 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.

Access to genetic testing in a state setting in South Africa is limited but is expanding due to its importance. New-born screening is not typical hospital procedure in South Africa and is not widely available. Due to a lack of policy, most medical insurers don’t reimburse for screening. An estimated 1% of infants get screened.

Notable projects

Notable organisations and companies

Notable individuals

  • Linda-Gail Barker: Barker isCOO of the Desmond Tutu HIV Foundation and former President of the International AIDS Society. In 2009, she won the Royal Society Ofizer 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 Professor of Public Health at the University of Witwatersarand. Her work has focused on cervical cancer, health systems and developing African capacity for public health research.
  • Tulio De Oliveira: Oliveira is 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 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 Professor of Human Genetics at the Institute of Cell and Molecular Science at Queen Mary, Unniversity 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 health care 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 have been developed outside of Africa and researched on a different gene pool. Drug failure and adverse side effects could be curbed by better understanding 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.

References

  • Paul Adepoju. African coronavirus surveillance network provides early warning for world. Nature. 2022.
  • Michele Clarke. Critical shortage of doctors in SA. Democratic Alliance. 2022.
  • Copenhagen Consensus Centre. South Africa Perspectives: Tuberculosis. Copenhagen Conesus Centre. 2022.
  • FEDUSA. Cheka Impilo to support the 90-90-90 strategy this World AIDS Day. Federation of Unions of South Africa. 2020.
  • University of Washington. Healthcare access and quality profile: South Africa. Health Data. 2016.
  • Chris Vorster. The case for newborn screening in South Africa. PathChat. 2013.
  • World Health Organisation. Scaling up genomic sequencing in Africa. WHO Africa. 2021.

Check out some of our other World of Genomics pieces:

Image credit: canva

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