Genomics Medicine: South Africa
This installment of World of Genomics Medicine delves into the intricate workings of South Africa’s healthcare system, its diverse population, and its rapidly expanding genomics capabilities.
With decades of underfunding and inequality still being felt, South Africa faces many difficult issues. South Africa, which has high rates of HIV and tuberculosis, is working to lower its disease load through cutting-edge genomics research and medical improvements. Leading the way in COVID-19 genome sequencing, the nation is advancing genetic research and healthcare to new heights.
The South African populace
Africa’s southernmost nation is South Africa. Namibia, Botswana, and Zimbabwe are its northern neighbours; Mozambique and Eswatini are its eastern neighbours; and it encircles the nation of Lesotho. Its southern shore, meanwhile, runs parallel to both the Indian and South Atlantic oceans.
Some of the world’s oldest archaeological and human-fossil sites are found in South Africa. The Gauteng Province is known as the “Cradle of Humankind” and is a UNESCO World Heritage Site. According to these findings, South Africa has been home to modern humans for at least 170,000 years, and a variety of hominid species have lived there since Australopithecus africanus approximately three million years ago.
Bantu-speaking peoples were among the greatest groupings during the Iron Age. Before South Africa became a British colony in the 1800s, it was colonised by the Dutch in the 1600s. In 1931, South Africa attained complete sovereignty.
Regular elections have been held for nearly a century, and the nation is among the few in Africa to have never had a coup d’état. But voting rights were not granted to the great majority of black South Africans until 1994. In South Africa, apartheid was a system of institutionalised racial discrimination that persisted from 1948 until the early 1990s. Non-white South Africans were denied basic human rights, including the ability to vote, by this system. Apartheid ended after a protracted and bloody fight by anti-apartheid campaigners both domestically and abroad, but its social and economic ramifications are still felt today.
South African healthcare system
Public health care was given priority under South Africa’s new health care strategy after the country ended apartheid.
Private and public health systems coexist side by side in South Africa. The majority of people are served by the public system. The National Department of Health, provincial health departments, and municipal health departments each have different levels of authority and responsibility for providing services. With just 0.91 physicians per 1,000 population, South Africa suffers from a severe shortage of medical personnel (2017). While 70% of doctors work in the private sector, all medical education is provided in public institutions.
The Uniform Patient Fee Schedule (UPFS), which classifies the various costs for each kind of patient and circumstance, is used by the public sector. Patients are divided into three categories: those who pay in full, those who receive full reimbursement (those referred to a hospital by Primary Healthcare Services), and those whose costs are only partially covered by insurance.
South Africa’s Universal Health Coverage in 2020 was evaluated at 52, compared to the global average of 57. By health index score, South Africa’s healthcare system was placed 56th in the world in 2021.
With continuous attempts to alleviate the nation’s healthcare disparities and enhance access to medical services, South Africa has made progress in its healthcare system as of 2023. The government’s healthcare reforms have centred largely on the National Health Insurance (NHI) system. The NHI seeks to establish a single National Health Insurance Fund supported by general taxes and contributions from health insurance, however its exact specifics are still being worked out. The aim is to lessen inequalities between various socioeconomic categories and give all residents equitable access to healthcare.
South African Health priorities
With the exception of COVID-related mortality, the most common causes of death in South Africa in 2020 were HIV, diabetes, cerebrovascular illnesses, tuberculosis, and hypertensive disorders.
As of June 2022, the nation had registered 101,859 COVID-19 fatalities and 3.99 million confirmed cases. The AU named President Cyril Ramaphosa its “COVID-19 champion” in recognition of his valiant efforts in containing the pandemic. It is noteworthy that the pandemic occurred less than a year after the first Presidential Health Compact was signed, outlining a five-year plan to achieve universal health coverage (UHC) by 2030. Resources from public health budgets were diverted to combat the virus as a result of the COVID-19 pandemic and lockdowns that followed, severely disrupting the AU’s public health order and causing an economic downturn.
In order to expedite the implementation of the National Health Insurance (NHI) programme, President Ramaphosa highlighted 10 major areas for intervention during the 2nd Presidential Health Summit in Johannesburg in May 2023. Human resources, access to medications and vaccines, infrastructure planning, private sector involvement, public sector financial management, community involvement, health information systems, leadership and governance, and pandemic preparedness were all covered in these areas.
The NHI is intended to provide funding for a healthcare system that provides South Africans with high-quality care according to their needs rather than their financial situation. The programme incentivizes the use of public health care and pushes the wealthiest people to contribute to the public system. However, there are still problems with resource distribution in the existing healthcare system. Only 18% of people use private healthcare providers, but the private health sector bears a large portion of health expenses through out-of-pocket payments and medical programmes. Furthermore, there are differences in access to care because 79% of physicians work in private practices.
The demographic makeup of South Africa bears witness to a history of persistent inequality. Black South Africans dominate every age category, but as the population ages, their share of the population declines. South Africans who are coloured, Indian, and particularly white typically have longer life expectancies. The AIDS epidemic of the 1990s and 2000s may be the cause of the dent in the population pyramid at ages 10 to 24. Roughly 9.2% of people are 60 years of age or older, while 28.3% of people are under the age of 15 (2021). The percentage of senior citizens is steadily rising, which means that policies and programmes that cater to their requirements must be given top priority.
HIV/AIDS has been one of the biggest obstacles to South Africa’s healthcare system. The nation is responsible for 17% of all HIV infections worldwide, although making up only 0.7% of the world’s population. But since 2021, there have been significant advancements, with a considerable proportion of HIV-positive individuals now obtaining antiretroviral medication. The availability of PrEP and initiatives like their multi-disease national wellness programme (2018) have improved HIV management and resulted in a 51% decrease in new infections between 2010 and 2021. According to data from March 2023, 94.2% of South Africans are aware of their HIV status.
In South Africa, tuberculosis (TB) continues to be a serious public health issue. The government is committed to screening 90% of people who are at risk as part of its continuous efforts to diagnose and treat tuberculosis. Multi-drug resistant tuberculosis (TB) still poses a challenge, nonetheless, as it represents 1.8% of new cases. It is still imperative to improve diagnostic methods, particularly for cases of drug-resistant tuberculosis.
The significance of treating chronic illnesses, such as malignancies, is also becoming more widely acknowledged in South Africa. The nation’s database and capacity to handle cancer cases have increased since the formalisation of cancer as a notifiable condition under the National Health Regulations in 2012. Due to the competing burdens of sickness in South Africa, cancer and other chronic illnesses were not seen as priorities in the nation.
Capabilities of genomics medicine
2021 saw the establishment of the Regional Centre of Excellence for Genomic Surveillance and Bioinformatics in South Africa. Southern Africa saw a quadrupling of genome sequencing activity between 2021 and 2022.
The world was first made aware of the Omicron SARS-CoV-2 strain by South African labs. The mutant variation was initially discovered in sequencing data from Botswana by the Network for Genomic Surveillance in South Africa.
South Africa is home to the African Pathogen Genomics Initiative facility. With almost 70,000 viral genomes sequenced by the network, it is clear that the nation is making quick progress in building up its sequencing capabilities to bolster genomic surveillance and support public health responses.
The Oxford University–AstraZeneca vaccine’s poor performance against the Beta type of SARS-CoV-2, which was the predominant variation in circulation at the time, led South Africa to discontinue the vaccine’s distribution in February 2021. In order to choose a vaccine, it would not have been feasible to identify the main viral variations that were circulating in the community without the sequencing capacity. The decision of South Africa to adopt COVID-19 vaccinations from Pfizer and Johnson & Johnson was based on genomic data.
When it comes to identifying illnesses like cystic fibrosis (CF) in their early stages, early screening is essential. Less than 600 instances of CF have been reported in South Africa to date, although specialists think this figure is much lower than the true number of cases. Sadly, the majority of CF-affected newborns in the nation remain undetected, which contributes to their early death from infections and problems associated with the disease. The issue is exacerbated by the lack of knowledge about cystic fibrosis (CF) among medical professionals, the lack of a programme for screening newborns, geographical barriers to receiving diagnostic services, and the similarities between the symptoms of CF and more prevalent illnesses like tuberculosis, HIV, and malnutrition associated with poverty. As a result, a large number of CF babies in South Africa might not receive a diagnosis before passing away from complications brought on by malnutrition as a result of untreated CF. According to consensus recommendations, in South Africa, the cystic fibrosis gene is present in about one in 27 persons of “Caucasian” ancestry, one in 55 people of mixed ancestry, and one in 90 people of black African heritage. These recommendations state that patients who have two positive sweat test findings ought to be referred for genetic testing in order to determine the exact genes involved and confirm their diagnosis.
In South Africa, access to genetic testing in the state context is currently restricted but is gradually increasing because of its increasing importance. Regretfully, newborn screening is still comparatively unavailable and is not a routine hospital procedure in the nation. The majority of medical insurers no longer pay for screening expenses as a result of the absence of support from policymakers.
The landscape of genetics medicine in the future
Concerned about inequalities in the current healthcare system, such as unequal access to care for different socioeconomic groups, the government is attempting to develop a national health insurance (NHI) programme. One theory regarding the NHI is that it will suggest creating a single National Health Insurance Fund to provide health insurance, even if the proposal’s specifics and general framework are still unknown. It is anticipated that ordinary taxes and some form of health insurance payment will provide funding for this fund. Genomics medicine
Building capacity and enhancing infrastructure for genome research in Africa is the focus of the Human Heredity and Health in Africa (H3Africa) Project. South Africa is home to several H3Africa bioinformatics nodes. These databases will shed light on global studies of human variation, partly because Africans have a high degree of genomic variety, which may reveal connections to diseases.
The SAMRC Genomics Center’s mission is to reduce South Africa’s illness burden by using an Afrocentric approach and expanding the country’s capacity for whole human genome sequencing. Key priority include infectious diseases, especially HIV/AIDS and tuberculosis, and lifestyle disorders like cancer, diabetes, heart disease, stroke, and hypertension. Genomics medicine
Nowadays, South Africans are exposed to medical research conducted on a distinct gene pool and produced outside of Africa. Gaining more knowledge about the effectiveness of drugs in the South African population could help prevent drug failure and unfavourable dosage effects. Future developments in genomics in South Africa will mostly be driven by the need to increase the diversity of genomic data and deepen our understanding of priority diseases.