In South Africa, a country known for its ethnic diversity and population of approximately 60 million, genomic sequencing has accelerated at a remarkable pace in recent years. And the impact has already been significant.

During the COVID-19 pandemic, for example, genomic sequencing was used to identify which vaccines would be most effective against the main variant infecting the population at the time, and South African labs analyzing wastewater were among the first to detect the Omicron SARS-Cov-2 variant and flag it for global awareness and action.  

But it’s not only in emergency contexts where genomics research has potential. Everyday treatment of prevalent illnesses is also a key focus area, with the aim of reducing South Africa’s burden of disease and beginning to develop medicines that are both researched on a local gene pool and produced closer to home.

Pioneering precision medicine

The South African Medical Research Council (SAMRC), established in 1969 under the supervision of the South Africa National Department of Health, is at the forefront of this effort. Its long-time focus on precision medicine eventually led to the development of the SAMRC Genomics Platform in 2019, a facility dedicated to the study of African-specific genomes for the purposes of creating solutions tailored to the healthcare needs of the local population.  

Professor Craig Kinnear, Director of the SAMRC Genomics Platform, explains, "We wanted to make genomics more accessible to South African researchers as the basis for developing individualized treatment strategies for patients. We needed a partner that has experience and knowledge in precision medicine and BGI was a natural fit, with many researchers in South Africa already working with BGI.”

 Professor Craig Kinnear, Director of the SAMRC Genomics Platform

Describing the partnership with SAMRC, Ronnie Mao, BGI Business Manager of South Africa, said, "We collaborated with SAMRC to identify the needs of the center and provided the equipment, training, and technical support to ensure its smooth functioning.”

Applying genomics technology

Through the partnership with BGI Group, SAMRC aims to develop precision medicine programs to treat well-known illnesses such as tuberculosis, diabetes, cerebrovascular diseases, HIV and hypertensive issues, as well as identify and serve those with rarer diseases who may not otherwise receive sufficient care.

Sequencing technology is key to this, as it enables analysis of an individual’s genetic makeup for healthcare professionals to tailor treatment plans and interventions accordingly. This, in turn, promises to improve patient outcomes and reduce complications flowing from the use of suboptimal medications.

Advancements in these areas are particularly relevant to rare disease diagnosis, given the complex and often elusive genetic origins of this category of ailments. With the ability to study an individual’s genome, genetic mutations associated with rare diseases can be identified, leading to early detection, greater diagnostic accuracy and appropriate management strategies for patients. Speaking to the issues around rare disease patients going undiagnosed or misdiagnosed, Professor Kinnear adds, “Genomics is there to help us identify these patients and provide them with the necessary support.”

As was seen during the COVID-19 pandemic, greater genomics sequencing capabilities in South Africa can lead to better infectious disease surveillance and outbreak management. With greater insight into the genomes of pathogens, healthcare professionals can more effectively track the spread of diseases and their transmission dynamics, as well as implement public health interventions to better ensure the health of society.

Describing a notable SAMRC undertaking in this area, Professor Kinnear said, “One of the biggest projects we've been involved with over the last three years was wastewater surveillance for COVID-19. We were also able to show, for example, how Omicron was detected at Cape Town International Airport in a sample that was collected even before it made international news.”

These developments also have a knock-on effect in pharmacogenomics, which examines how an individual’s genetics influences their response to medications. Through analysis of genetic variations related to drug metabolism and efficacy, the right medication, dosage and treatment plan can be identified on a per patient basis. During the pandemic, this was seen on a larger scale through the preference for the Johnson & Johnson and Pfizer vaccines over the Oxford University-AstraZeneca one. Based on local genomic data, the latter was found to be inefficient against the Beta variant which was prevalent at the time.

 Ronnie Mao works with Professor Kinnear in the SAMRC lab.

Progress through partnership 

While much progress has been made across South Africa in establishing genomics infrastructure, more capacity building is needed to continue this momentum. Describing how its partnership with BGI Group is achieving this, Professor Kinnear stated, "BGI has donated a third large sequencer to our platform, and their continuous technical support has been invaluable." Giving South African researchers and healthcare professionals access to cutting-edge genomics technology and training is indispensable for further innovation and progress.

And SAMRC has more planned on the horizon. Professor Kinnear added, “Continuing our partnership with BGI Group, we are embarking on a diagnostics arm for our facility. We hope that our future collaboration will be even more fruitful.” This focus on diagnostics will be key to addressing South Africa’s various healthcare challenges and protecting the wellbeing of its citizens.

Growing South Africa’s capacity for Next Generation Sequencing requires the right partners, technology and know-how. Signalling what the SAMRC Genomics Platform can expect going forward, Ronnie Mao said, “BGI Group is committed to continuing its collaboration with South Africa to advance scientific research and improve health outcomes. Whether it’s through training or technical support to researchers and healthcare professions, we want to ensure our partners have access to the latest genomics technology.”

This commitment means a greater potential to transform the way healthcare is approached and experienced – being more personalized, targeted and reliable – all through the growing promise of genomics research.