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Let’s be Pragmatic – the NHI has Constructive and Contentious Aspects

On By ModernMedia

By Susan Cleary for Spotlight

Professor Susan Cleary delivering her inaugural lecture as part of a lecture series by the University of Cape Town. (Photo: Supplied)

President Cyril Ramaphosa recently signed the NHI Bill into law. The question is whether this will bring South Africa closer towards Universal Health Coverage. Professor Susan Cleary argues that the NHI is a wide ranging reform with both positive and controversial aspects. The key will be to find a middle ground in order to continue on the journey to UHC.

President Cyril Ramaphosa signing the National Health Insurance (NHI) Act on the eve of the elections is a smart move from the perspective of a political party seeking to shore up its base. The concern though to those of us working to strengthen the health system is whether the NHI will enable the country to move closer towards Universal Health Coverage.

For the NHI naysayers, perhaps it would be important to alleviate some fears and concerns. The NHI is a long-term project. In the 2024 budget, National Treasury reduced the conditional grant allocations to the NHI in comparison to what was allocated in the 2023 budget. While signing the NHI Bill into law is a step forward, the reduction in resources towards NHI implementation reminds us that this is a long term project. In addition, it is likely that there will be legal challenges which will lead to considerable delays for the scheme to be fully implemented.

The NHI is a wide-ranging reform, with many positive aspects sitting alongside some key controversial aspects. Positive aspects include the opportunity to enable greater use of evidence and transparency in priority setting through the further institutionalisation of Health Technology Assessment processes (akin to ‘NICE’ in the UK), as well as the opportunity to use national-level purchasing power to drive down the prices of commodities such as medicines. The role of private multidisciplinary practices (GPs, nurses, health and rehabilitation professionals, etc) in the future NHI also holds some promise to improve access to healthcare particularly to parts of the country with limited access to public clinics.

On the other hand, there are two key controversial aspects. The first is related to what may or may not happen to medical schemes and medical scheme administrators once the NHI is fully implemented. My sense is that there is no short-term concern in this regard. A bigger concern is whether a single pot of money in the NHI fund will present a larger or a smaller corruption risk than the current situation of multiple pots spread across provincial treasuries and medical aid schemes.

Another concern is that the NHI reform might disrupt our ongoing progress towards Universal Health Coverage within our existing public sector. Our public sector is not perfect, but it is a system that has equity at its heart. The common definition of Universal Health Coverage is to provide all individuals and communities with access to needed promotive, preventive, resuscitative, curative, rehabilitative and palliative health services of sufficient quality to be effective, while ensuring that the utilisation of these services does not expose users to financial hardship.

The two main goals of Universal Health Coverage are: (1) the provision of quality health care services to those in need and (2) the avoidance of financial catastrophe in this process. Clearly healthcare is far from free – indeed it is very expensive – and so the goal of avoiding financial catastrophe is about implementing prepayment and risk pooling mechanisms, whether these are tax or insurance based.

Let’s first look at how we are doing on the provision of quality services. The below figure plots countries according to their achievements on the Universal Health Coverage Service Coverage Index. In this context, coverage of essential health services is measured based on indicators that include reproductive, maternal, newborn and child health, infectious diseases, non-communicable diseases and service capacity and access, among the general and the most disadvantaged populations.

On this index, South Africa’s achievement is at just over 70%, similar to many other middle-income countries. While there would be room for improvement, our performance is in line with our global peers.

Global comparison of countries in terms of service coverage and quality

Source: World Health Organization – Global Health Observatory (2024) processed by Our World in Data. Accessed May 2024.

The second indicator is financial risk protection. The below figure plots countries against the percent of total health expenditure that is paid out of pocket at the point of use. On this indicator, we score 5.7%, indicating extremely high levels of financial risk protection.

Global comparison of countries in terms of the percent of total health expenditure that is paid out of pocket

Source: World Health Organization (via World Bank) processed by Our World in Data. Accessed May 2024.

While this does not mean that there are no instances of financial catastrophe, undoubtedly there would be, particularly for those seeking treatment for certain types of cancers. That said, over the past two decades I have studied this issue extensively. Across a wide range of conditions in diverse settings, we have interviewed tens of thousands of people to understand the costs that they face in using health services, including everything from transport costs, to costs of food, shelter or accommodation, costs of child care, lost income, under the counter payments to public sector providers (which we never found), fees paid to private providers or money spent at pharmacies. This research consistently showed that the level of catastrophic spending was very low. Our performance on financial risk protection is outstanding. I celebrate the work of those colleagues that shepherded in the removal of user fees in our national health system during the dawning of our democracy. We should all be thanking them.

Despite these successes on Universal Health Coverage, there are areas of concern for the South African health system. We do not achieve health outcomes commensurate with our level of investment. My sense is that this is driven by our relatively high burden of disease; for example we continue to have the world’s largest HIV treatment programme. While our average life expectancy steadily increased with the introduction of antiretroviral therapy (although note the downturn from 2020 which coincides with the Covid-19 pandemic – see the below figure), the HIV epidemic has been a cruel setback that needs to be considered when we seek to make global comparisons on life expectancy and avertable mortality.

Global comparisons of life expectancy: 1970 – 2020

Source: United Nations World Population Prospects (2022) processed by Our World in Data. Accessed May 2024.

Now that the NHI Bill has become the NHI Act, it is time to move on from debates about whether we need NHI or not, and rather focus on how we can make the NHI work for us.

Our public sector will be the backbone of our future NHI and so we should seek to continue to strengthen this system. It would also be wise to put in place measures to strengthen our private system given that private providers are intended to play a key role in the NHI. We should be pragmatic.

The NHI includes many exciting opportunities for leveraging big data and artificial intelligence in health systems strengthening, but at this stage we hardly have any electronic health data. A clear step forward would be the further implementation of the National Digital Health Strategy (2019-2024) which includes the establishment of a patient electronic health record, amongst other needed developments.

In addition, the NHI places emphasis on the achievement of a purchaser provider split via establishing ‘Contracting Units for Primary Health Care’ (CUPS). These new entities will contract with both public and private providers within a defined geographic area, on behalf of a particular population. The establishment of CUP ‘proof of concept’ sites is therefore a priority, but must be done in a way that generates learning and enables adaptation to different contexts.

Let’s continue to push forward on many of these complex undertakings. It is going to take time, but it is needed, irrespective of the name that we choose to give to our health system.

*Cleary is professor of health economics and the head of the School of Public Health at the University of Cape Town.

Note: The views expressed in this opinion piece are not necessarily shared by the Spotlight editors. Spotlight is committed to publishing a variety of views and facilitating informed discussion that deepens public understanding of health issues.

Republished from Spotlight under a Creative Commons licence.

Source: Spotlight

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PhD Research Explores Precarious Balance of Sleep, Light and Sedentarism among Gamers

On By ModernMedia
Photo by Igor Karimov on Unsplash

By Helen Swingler

With frequent and long stints at their computers, the average gamer is a sedentary night owl, often compromising on sleep – especially quality sleep – and being exposed to too much blue light. The topic has been explored in University of Cape Town (UCT) PhD candidate Chadley Kemp’s doctoral thesis, a meaty study of over 70 000 words.

Kemp’s research into habitual gaming activities is supervised by Associate Professor Dale Rae, a sleep researcher and senior lecturer at the Health Through Physical Activity, Lifestyle and Sport Research Centre (HPALS) in the Faculty of Health Sciences.

This work is founded on Kemp’s 2018 research underpinning a master’s in medical science at UCT’s former Department of Exercise Science and Sports Medicine in the Sports Science Institute of South Africa. This was upgraded to a PhD in 2020.

His research (he is an esports and video game enthusiast) explores adult esports players’ sleep, health status, light exposure patterns and physical activity.

“We know that sleep affects mental functioning in general, but we weren’t sure about the extent to which this applied to esports players,” said Kemp.

Framework for healthier gameplay

Kemp’s goal is to produce objective data that will guide the development of a framework aimed at promoting healthier gameplay standards and encouraging policy reform within the esports industry.

The tests they used to assess neurocognitive performance were intended to serve as proxies for certain aspects of esports performance because they tested specific mental skills important to gaming, he added.

“We gathered it would be a useful addition to compel gamers to adopt better sleep and lifestyle behaviour changes if it meant … that their health would improve, and they would benefit from better in-game performance – and get an edge over their competitors!”

Kemp’s focus is not on professional gamers, but what he calls “the missing middle” of the esports community: the amateur and semi-competitive gamers.

“This group doesn’t have the same infrastructure and support as their professional counterparts,” he explained. “But what makes them particularly interesting is the fact that they have to balance their gaming commitments with holding down a job, studies, or juggling family or household commitments.”

Global attraction

Esports are burgeoning across the globe – and not only among competitive gamers but audiences too. Writing in the South African Journal of Sports Medicine, Kemp and his co-authors noted that globally competitive gaming attracts 532 million fans alone, according to statistics released in 2022.

However, his study wasn’t motivated by an influx of gamers presenting themselves with sleep difficulties at Associate Professor Rae’s sleep consultancy, Sleep Science. Rather, it stemmed from a broader observation and concern within the local esports community about gamers and poor-quality and short-duration sleep, high levels of sedentarism, and excessive exposure to artificial or electronic night at night.

Based on these conversations and endorsed by anecdotal evidence from within the esports industry, Kemp said he and Rae were able to determine that sleep curtailment had seemingly become a “rite of passage” among gamers. Primarily, most gaming takes place at night because of gamers’ daytime commitments.

As there wasn’t much literature on the topic (much of it is focused on the implications of gaming in children and adolescents) and most studies were survey-based and didn’t target esports players or those regularly engaged with gaming, there was significant knowledge gap that needed filling. As a demographic, Kemp is particularly interested in adult esports players because of the greater health risks posed by age and unhealthy lifestyle factors, such as smoking and alcohol consumption.

Because he needed a tool to measure sleep and physical activity concurrently, he validated the Actiwatch, a special research device, to do this. The device also measures light exposure. For his sample group, Kemp recruited eligible esports players and measured variables of interest. These were clinical measures (anthropometry, blood pressure, blood markers) and self-report data (questionnaires on sleep, chronotype, daytime sleepiness and gaming addiction) and their cognitive performance.

“We also included non-gamers in our study, so we could compare our gamers against people who were not gamers. In total, we had 59 male participants (31 gamers; 28 non-gamers). (The females volunteering to participate did not meet the study’s inclusion criteria.) For a week, these individuals wore the Actiwatch to track their sleep, physical activity, and light exposure.”

Key findings

The key findings of his research make for interesting reading:

  • esports players have comparable sleep duration to non-gamers (control group) but tend to sleep later than others. They hit the middle of their sleep cycle around 04:08 compared to 03:01 for the control group.
  • A much larger percentage of esports players (45.2%) showed night-oriented habits (or evening chronotypes), ie they are more active and alert at night. This is in contrast to only 7.1% of the control group showing similar evening tendencies.
  • They nap more during the day, but their night sleep duration is similar to that of the control groups.
  • There was no significant difference in risks related to heart diseases or metabolic diseases between the two groups, which Kemp speculates might be related to their young age. But most of the health markers were tentatively raised, which could point to worse cardiometabolic health in future.
  • Esports players smoke more.
  • Esports players performed better in brain-based tasks, showing better attention and accuracy, and making fewer mistakes.
  • Esports players are less active than the control group. They sit more (11.2 vs 9.1 hours a day) and are less physically active, whether it’s moderate- or vigorous-intensity activity.
  • Esports players have specific active and inactive hours. They are less active in the early morning and certain evening hours but are more active around midnight.
  • Esports players are exposed to dimmer light for a more significant part of their day, and their exposure to bright light happens later at night.

This work is important for several reasons, said Kemp. A key takeaway from the research revolves around chronotypes.

“Esports players seem to have sleep patterns that align with being night owls and this may be influenced both by their natural tendencies and their gaming habits. It’s also possible that a genetic disposition and exposure to artificial light from screens collectively contributes to these sleep patterns.

“The combined effect is thought to create a cycle where their preference for evening activities leads to more gaming, which in turn reinforces the night owl tendencies. This impacts on their sleep quality and quantity.”

He added: “Perhaps more obviously, gaming is a massively popular phenomenon that transcends age, sex, and geography. It’s a dominant form of entertainment and its competitive arm, esports, is progressing towards acceptance as a genuine form of sporting competition.”

From the neurocognitive side, it’s clear that gaming can sharpen several cognitive abilities, such as attention and problem-solving.

“However, the catch is, if you’re not getting enough sleep, these enhanced skills could take a hit,” said Kemp. “Gamers might see slower reactions, flawed decision-making, and even a drop in their in-game stamina. So, while gaming certainly has its merits and can even boost certain mental skills, it doesn’t come without health considerations. “

Kemp’s research is aimed at ensuring that anyone engaged with gaming or esports does so in a healthy way.

“The purpose is to create a steppingstone towards health regulation in gaming and esports,” he said. “By creating awareness and providing evidence-based recommendations to prevent chronic health problems caused by unhealthy gaming behaviour, it supports individual decision making, governments, and policy makers. It’s valuable to anyone involved in or impacted by gaming.”

Kemp’s guidelines for gamers:

  • Get between seven and nine hours’ sleep a night and keep a regular sleep schedule (on weekends too).
  • Set fixed waking and sleep times to establish a more robust sleep–wake cycle.
  • For better sleep, ensure your bedroom is dark, quiet, and cool (16-18°C is optimal).
  • Limit the amount of light exposure in the hours before bedtime (including light from phones, laptops, TVs, etc).
  • Limit caffeine to the morning and afternoon. This means no energy drinks during those night-time gaming sessions).

Republished from University of Cape Town under a Creative Commons Attribution-NoDerivatives 4.0 International License.

Source: University of Cape Town

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H3D’s Pioneering Research Adds Hope to the Fight against Malaria 

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Members of the University of Cape Town’s Holistic Drug Discovery and Development Centre H3D

A formidable disease that has plagued humanity for centuries, malaria has exacted a heavy toll on human lives, disrupting communities and hindering socio-economic progress across some of the most vulnerable regions of the world, particularly the African continent.  

With its stealthy transmission through the bites of infected mosquitoes, malaria has earned the dubious reputation of being one of the deadliest vector-borne diseases on the planet. So much so that the World Health Organization’s World Malaria Report reveals that malaria cases are on the rise, with instances rising from 245 million cases in 2020 to over 247 million a year later1. 

With an estimated 619,000 people succumbing to the disease in 20211, it remains a defining challenge for global healthcare systems. However, through the unyielding persistence and spirit of medical innovation and scientific ingenuity exemplified by research facilities such as the University of Cape Town’s Holistic Drug Discovery and Development Centre (H3D), solutions to mitigate the severity of malaria are on the horizon.  

“As the first and only integrated drug discovery platform on the African continent, H3D’s mission is to discover and develop innovative life-saving medicines for diseases that predominantly affect African patients,” explains Bada Pharasi, CEO of the Innovative Pharmaceutical Association of South Africa (IPASA).

H3D’s focus on building Africa-specific models aims to improve treatment outcomes in African patients and to educate and train a critical mass of skilled African-based drug discovery scientists. H3D’s scientific output and research model includes attracting international investment in local innovative pharmaceutical research and development (R&D) across the African continent to address the disproportionately high global disease burden. Importantly, H3D targets critical infectious diseases, including tuberculosis, antibiotic-resistant microbial diseases, and malaria. 

“Given the vulnerability of many of the African populations, the continent accounted for 95% of malaria cases and 96% of malaria deaths in 20211. Accordingly, continued antimalarial drug research and development, such as the studies conducted by H3D, is important to prevent and treat the millions of cases that arise each year, all of which have consequences on both the health and socioeconomic development of the continent,” adds Pharasi.

Since the official launch of H3D’s programs in April 2011, there have been notable advances in innovative drug discovery projects. The centre has demonstrated a strong track record with multiple chemical series discovered and being progressed at H3D in each stage of the drug development pipeline.

A significant achievement reached by H3D was the discovery of the malaria clinical candidate, MMV390048, which reached phase II human trials in African patients. This was the first ever small molecule clinical candidate, for any disease, researched on African soil by an African drug discovery research unit. 

According to Dr Candice Soares de Melo, Chief Investigator at H3D, the centre’s current anti-malarial programmes will focus on the identification of quality leads suitable for optimisation and candidate selection as potential agents for the treatment of uncomplicated Plasmodium falciparum malaria, ideally with additional activity against liver-stage parasites to offer protection and prevent relapses (in case of malaria caused by the species Plasmodium vivax), as well as blocking the transmission of the disease. 

“A critical component of the research conducted at H3D is to develop medicines that are safe and sufficiently tolerated to be given to the widest range of recipients, including infants and pregnant women,” says Soares de Melo.

Besides the potential benefits of providing a new cure for malaria, H3D serves as a catalyst for training scientists in infectious disease research and influencing the R&D environment in Africa.  As part of its partnership with the South African Medical Research Council, H3D has worked to mentor and develop scientists at other African universities, including those at Historically Disadvantaged Institutions (HDIs) within South Africa. 

Furthermore, apart from strengthening drug discovery innovation at UCT, the centre has also taken a lead role in partnership with the Bill & Melinda Gates Foundation in catalysing drug discovery across sub-Saharan Africa, with upwards of 16 university research groups working on malaria and tuberculosis drug discovery. 

“An example of this is the Phase 1 clinical trial for the H3D clinical candidate MMV390048, which was carried out at the UCT Division of Clinical Pharmacology,” adds Soares de Melo. 

Another is the MATRIX independent special project, which has the potential to transform local drug manufacturing across the continent. Funded by the United States Agency for International Development (USAID), the project aims to pilot cost-effective local manufacture of antiretroviral Active Pharmaceutical Ingredients using flow reactor technology.

“Should Africa intend on a path to self-sufficiency, it’s important to drive continued investment in health innovations developed for and by Africa.

“We support the research efforts of H3D, and strongly believe that now is the time to take a deliberate and systematic approach to develop new capabilities, transfer technologies, leverage partnerships and networks, and train scientists, all while delivering on drug discovery projects to help address the continent’s, and the world’s, greatest health challenges,” concludes Pharasi.

For more information, visit https://h3d.uct.ac.za/ or contact Candice Soares de Melo at candice.soaresdemelo@uct.ac.za.

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Interview: “The Only Good TB Bacillus is a Dead One”, Says UCT’s Prof Valerie Mizrahi

On By ModernMedia

By Biénne Huisman for Spotlight

Professor Valerie Mizrahi, a world-leading tuberculosis researcher and director of the Institute of Infectious Disease and Molecular Medicine at the University of Cape Town, is retiring at the end of the year. PHOTO: Nasief Manie/Spotlight

World-leading tuberculosis researcher Professor Valerie Mizrahi was 35 when her mother Etty started losing weight and coughing furiously. After healthcare professionals in Johannesburg failed to accurately diagnose her, it was a doctor in Plettenberg Bay who told Etty: “The good news is you don’t have lung cancer, the bad news is that you have tuberculosis (TB).”

At the time, Mizrahi’s two infant daughters – aged one and three years old – had been spending much time with their granny. And so Mizrahi found herself crushing TB prevention tablets into her children’s porridge with honey.

Etty was treated at the then-Rietfontein Hospital, the precursor to Sizwe Tropical Diseases Hospital in Johannesburg. “My mom got very ill,” recalls Mizrahi. “She almost died of TB. And then 10 years later, she had to have a lobe from one of her lungs removed because she was one of those unfortunate people who got post-TB fibrosis.”

This was the early 1990s. Mizrahi was then with the South African Institute for Medical Research (SAIMR) linked to the University of the Witwatersrand, where she established the Molecular Biology Unit. She had identified TB as a lurking problem in South Africa, particularly in mines and in hospitals, calling it “a worthy foe ripe with opportunity for scientific investigation” – a problem she felt not enough people were talking about. It had been a pivotal moment when TB entered her own home, one that she says galvanised her thinking.

“It was a dramatic eye-opener for me as a basic scientist,” she says. “It was traumatic because of the time it happened in my career. Our family suddenly being thrust into the world of TB control. We had all these questions like we didn’t know where my mum got it, was her TB drug-susceptible, and why it would take so long to find this out. I got to see first-hand how difficult it was to get answers…”

Born in 1958 to Etty and Morris in Harare, Zimbabwe, Mizrahi studied at the University of Cape Town (UCT), forging an unusual career path, veering from mathematics and chemistry to biochemistry, genetics, and microbiology. In a male-dominated field, she became one of the first in South Africa to interrogate TB at a basic science level – that is to say, research aimed at advancing our understanding of the basic science of how TB bacteria survive, replicate, and resist attempts to kill it.

‘the only good TB bacillus is a dead one’

Discussing TB, Mizrahi’s passion is effervescent, her every second sentence punctuated with “okay”. These underscore her statements – subtle pauses allowing for her preceding words to sink in.

Source: CC0

…there’s a reason why TB has persisted for so long. The bacillus is pretty hard to kill. It’s built like Fort Knox.

Prof Valerie Mizrahi

A particular interest for Mizrahi is developing antibiotics “that can kill this bacterium stone cold dead”.

“To me, the only good TB bacillus is a dead one,” she says. “But there’s a reason why TB has persisted for so long. The bacillus is pretty hard to kill. It’s built like Fort Knox. So it’s a monumental challenge. We don’t know where all the bacteria are residing. We know that TB in an infected lung is sitting in really difficult places, hard places for drugs to get to. This notion of going after the bacillus with drugs and just slamming it is a tough problem. Not insurmountable, but there’s a lot of research that needs to be done.”

TB can be cured, but treatment typically takes at least six months and involves taking at least four different antibiotics, with side effects ranging from minor to serious. In addition to research on new antibiotics, there are also several experimental TB vaccines currently in late-phase studies. The only TB vaccine we have was developed more than a century ago and only has some moderate efficacy in kids.

The IDM

Since 2011 Mizrahi has served as director of the Institute of Infectious Disease and Molecular Medicine (IDM) – the University of Cape Town’s (UCT) largest cross-faculty research unit with over 800 affiliated staff and grants running into hundreds of millions of rands.

Mizrahi’s glass-encased office looks directly onto Table Mountain and hospital bend – where, at the time of our interview, N2 traffic out of Cape Town is already at a standstill. Behind her desk, Mizrahi quips. “Yes, this is the most beautiful office at UCT, everyone agrees…” Below, students can be seen milling about on the health sciences campus.

Last year in its Best Global Universities 2022-2023 survey, online portal US News ranked UCT as 24th best university in the world for studying infectious diseases. Mizrahi is ambivalent about the IDM taking credit for this accolade. She notes that this success is founded on problems of a “confounding and overwhelming” scope, with many diseases being proxies for poverty and inequality in South Africa.

The IDM’s focus includes TB, HIV/AIDS, COVID-19, other infectious diseases like sexually transmitted infections, and non-communicable diseases such as preventable cancers, cardiovascular, and psychiatric disorders.

Reflecting on the IDM, she says they have accrued a “research ecosystem – a concentration of expertise, something resembling critical mass” – bringing together specialists across the basic, clinical, and public health sciences, in one place.

“We’ve got Groote Schuur Hospital across the road,” she says. “We have geneticists and biochemists, virologists, and immunologists. There’s a clinician across the corridor from me, bioinformaticians, and microscopists downstairs. If you are the kind of researcher who revels in asking questions and finding people who can answer them, then this is the place for you.”

Going forward, multi-disciplinary research is what excites her. “HIV and TB have been so dominant in the narrative of this country. But now when you look at the figures and the data, we are dealing with a huge burden of non-communicable disease on top of infectious diseases,” she says. “The key question moving forward is how not to think in silos.”

Polymaths and dilettantes

This, she says, takes humility.

“To do this, one has to be very humble. You need to know what you don’t know. People who work really well in interdisciplinary spaces are those who understand the limits of their own specialist knowledge, and the need to listen to where another person is coming from.”

She distinguishes between polymaths and dilettantes. “You have to be careful not to be a dilettante, who knows a little about a lot. Research can be very superficial in that way. So I have my antenna out all the time to distinguish between polymaths, who really are people who know a lot about a lot, and dilettantes who know a little about a lot. And well, in this institute we have a lot of polymaths, brilliant researchers who move across disciplines, very interesting people to work with.”

With a string of awards and an A1-rating from South Africa’s National Research Foundation, earlier this year, Mizrahi was elected a fellow of the Royal Society, the United Kingdom’s National Academy of Sciences. However, she recalls humbling moments along the way – like the time she flew to London seven months pregnant with her second child, for her first-ever interview with the Wellcome Trust committee to secure funding. “I was so confident, but I was ill-prepared,” she says. “They savaged me! I tried to frame it not as a failure but as a learning experience.”

Passing the baton

At the end of this year, Mizrahi will pass on the baton when she retires. Of her achievements, she is proudest of young scholars she has helped to shape. “Their legacies will last much longer than a few more citations of a publication,” she says.

Mizrahi notes more and more women leaders in her field. For example, recently, while delivering a talk at the Weizmann Institute in Israel, she noticed chemist and Nobel laureate Ada Yonath in the room. “Talk about a role model; I was almost in tears.”

Studying at UCT, Mizrahi’s own mentors had mostly been men – something she didn’t even notice, she says, as male professors treated her no different. What did cut her was racial segregation at the time, prompting a political awakening and stints leaving South Africa to work in the United States. First as a postdoctoral fellow at Pennsylvania State University and then at drug company, SmithKline & French in Philadelphia.

Her own background makes her sensitive to marginalised groups, she says. Her grandparents were Sephardi Jews who fled Rhodes Island, today part of Greece, ten years before World War II, to find refuge in Zimbabwe.

Having just read former UCT vice-chancellor Max Price’s book Statues and Storms: Leading a University Through Change, she says, “It took me back to some very difficult times. It’s harrowing and brave and made me realise that even though I was here in the midst of it [#feesmustfall and #rhodesmustfall protests], a senior person of the university, how little I really knew of what was going on. It really is a lesson in crisis leadership.”

 There’s no control experiment to life, you can’t go back and redo it.

Mizrahi lives in Sea Point with her one daughter. Her other daughter is based in Vancouver. Here, she likes to park her car at the end of the week, walking around – “either listening to a New York Times podcast or a beautiful piece of music and that’s when I think.”

She describes herself as an introvert who needs personal time to stay sane. She is deeply thoughtful about her roots, wondering about a sense of belonging. “As white people in Africa, I think this is part of the reckoning we go through. I truly identify as being African. Arriving at Johannesburg, just breathing in the air, it feels like home.”

Looking back, Mizrahi notes her mother as a major influence in her life. “Not a highly educated woman. But the wisest, smartest person I know.” Etty still lives in Johannesburg while Morris has passed away. To this day, Etty thinks of herself as a proud TB survivor, says Mizrahi.

On her retirement, the scholar says, “Now it’s about opening up opportunities for others, writing a few papers, and contributing to the TB drug discovery space.”

“I’ve done the best I can,” she says, “I don’t believe in having regrets…  There’s no control experiment to life, you can’t go back and redo it. But I don’t know that I could have done it any differently.”

Republished from Spotlight under a Creative Commons Licence.

Source: Spotlight

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Med Student’s Stellar Academic Record Paves Way for Elective Abroad

On By ModernMedia

By NIÉMAH DAVIDS

Photo: Supplied

Fifth-year Bachelor of Medicine and Surgery (MBChB) student Moses Malebana’s stellar academic record has paved the way for a special international elective at the University of Graz – making him the maiden recipient of this golden opportunity – and galvanising ties between the University of Cape Town’s (UCT) Department of Medicine and the Medical University of Graz (Med Uni Graz) in Austria.

Malebana will depart in November and return to UCT’s Faculty of Health Sciences in January 2024. And with just a few short weeks before he boards his flight, he said he is excited for what awaits, and plans to absorb every detail of the experience.

“I plan on becoming a giant sponge while there. I am excited and feel privileged that I’ve been selected for this opportunity. I look forward to learning all there is to learn and flying UCT’s and the Department of Medicine’s flag[s] high at Med Uni Graz,” he said.

Tough grind

But this opportunity didn’t just fall into his lap. To be considered for the elective abroad, the application and selection criteria was clear – the candidate needed to prove an unmatched academic record. Each applicant was also tasked with supplying a motivational letter that highlighted why they felt they deserved the opportunity. It’s safe to say that Malebana passed the test with flying colours.

He said he used the motivational letter to reflect and relay personal anecdotes that focused on the sacrifices that led him to study medicine at UCT, and he enjoyed documenting his story.

“I remember seeing the email and thinking that this is my opportunity to reflect on my journey and to just tell my story. It was interesting because I don’t often reflect on things. But when I started, I realised that my whole life up to this point was about making the most of the opportunities that have come my way,” he said.

First-class motivation

In his motivation, Malebana touched on the events in his life that moulded him into the man he is today. And the list is endless – walking for more than an hour to and from school every day in rural Limpopo, contending with a lack of in-school resources, and a shortage of skilled teachers were just some of the challenges he experienced. These hurdles, he added, provided the impetus he needed to give his high school education and his medical studies his all.

“All of this taught me resilience; it motivated me to work even harder to reap the rewards later in life. I worked very hard to get to UCT, and now that I’m here, I’m working even harder to attain success in my degree,” he said. “I don’t take any opportunities for granted. I’m humbled that I’ve been chosen to represent the faculty and the university in Austria,” he said.

As he prepares for his big trip, Malebana said he’s looking forward to understanding the Austrian health system and gaining some valuable insight into how medical doctors practice medicine in that country and how it compares to South Africa.

A whole new world

The elective will consist of several rotations in different areas of internal medicine and Malebana will be based at a teaching hospital affiliated to Med Uni Graz. He said he is most excited about his oncology rotations after developing a keen interest in this area of medicine.

“I have always enjoyed studying and learning more about the management of different cancers. So, I really look forward to seeing how things are done in Austria. I know each day will be filled with something new to learn, whether it’s in oncology or a different area of medicine. I’m eager to get going,” he said.

But over and above the work, Malebana said he is thrilled to have the opportunity to travel outside of South Africa’s borders for the first time, to experience diverse cultures and cuisines, gain insight into a new way of life, and build new, lasting friendships.

“It’s going to be an adventure, that’s for sure – one that I’ve already embraced with my arms wide open. I’m grateful that it has come my way,” he said.

Republished from the University of Cape Town under a Creative Commons Attribution-NoDerivatives 4.0 International Licence.

Source: University of Cape Town

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Going Viral: Dr Chivaugn Gordon on Medical School with a Difference

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Dr Chivaugn Gordon, head of undergraduate education at UCT’s Department of Obstetrics and Gynaecology, reflects on her love of teaching future doctors about women’s health issues. PHOTO: Nasief Manie/Spotlight

By Biénne Huisman for Spotlight

With humour and wearing an occasional wig, Dr Chivaugn Gordon teaches medical students about serious women’s health issues. During hard lockdown she delighted students at the University of Cape Town (UCT) with educational videos using household items as props. For example, she created an endometrium (the inner lining of the uterus) from hair gel and red glitter, performed a biopsy on a potato, and showed a chicken hand puppet go into labour.

One video features a patient named Zoya Lockdownikoff – who is a spy – consulting with her doctor about abnormal menstrual bleeding. Gordon, in a blonde wig with round sunglasses, plays Lockdownikoff; and Gordon’s husband, Dr Adalbert Ernst, plays her doctor.

Lockdownikoff explains that the bleeding started when she “did a very complicated backflip to escape a very compromising situation” and that it’s ruining her expensive super-spy coats.

Gordon is head of undergraduate education at UCT’s Department of Obstetrics and Gynaecology, while Ernst is with the university’s Department of Anaesthesia and Perioperative Medicine.

Speaking from her yellow-walled lounge in Cape Town’s Bergvliet, Gordon says: “I became a doctor because I love working with patients. And then I realised, oh cool, I love teaching too. And now I can do these two things together.”

Interest in IPV

For Gordon a driving interest has been intimate partner violence (IPV) which she introduced into her undergraduate curriculum in 2015.

“The aim is to have graduating doctors who are able to recognise intimate partner violence. Everybody thinks that you can’t possibly be abused unless you have a black eye or a fractured arm. But actually, IPV is often more psychological. It’s often psychological abuse. So the challenge is to teach young doctors what are the red flags in someone’s behaviour, or in their clinical presentation, that might indicate IPV.”

Published online in April, Gordon delivered a talk for TEDxUCT called “Tackling IPV, one awkward dad conversation at a time”, in which she notes IPV is “a global pandemic that has been ongoing since time began”. The title refers to Gordon’s father who raised her.

According to a paper published in the journal Lancet Psychiatry last year, IPV is the most common form of violence worldwide; it is most prevalent in unequal societies, and its victims are mostly women and girls. The paper states that worldwide 27% of women and girls aged 15 and older have experienced physical or sexual IPV, but in South Africa the figure is estimated to be much higher, between 33 and 50%.

Gordon contributed to South Africa’s revised Domestic Violence Amendment Act of 2021, through UCT’s Gender Health and Justice Research Unit.

The new legislation broadens the definition of domestic violence to include (above and beyond physical and sexual abuse) emotional, verbal or psychological abuse, which is described as “a pattern of degrading, manipulating, threatening, offensive, intimidating or humiliating conduct towards a complainant that causes mental or psychological harm…including (repeated) insults, ridicule or name calling; (repeated) threats to cause emotional pain; the (repeated) exhibition of obsessive possessiveness or jealousy…”

Gordon highlights the term coercive control. “Because that underpins most serious intimate partner violence. So, somebody who is extremely controlling; they want their partner to do what they want, when they want, and how they want immediately. They normally start isolating you from friends and family so they can spin a narrative of your reality that can’t be contested by anyone else. And it also makes it more difficult to leave.”

Red flags

Gordon highlights some of the IPV red flags that doctors should look for in their patients.

“Depression, anxiety, PTSD, insomnia, [and] things like self-medicating with substances,” she says. “Because when you are living in absolute, abject terror every day of your life, it’s going to manifest in some kind of psychological manner. So, when people have been broken down and worn down and their self-esteem has been eroded it also affects the way they might interact with the healthcare professional.

“Big red flags come out in body language. Usually when someone goes to a doctor, they tell you everything about all their symptoms, because they want you to make them better. So, if you’ve got a patient who is closed off, they’re not making eye contact, they’re avoiding answering your questions, they’re just very reticent and you can’t get anything out of them…then you’ve got to think.”

Gordon stresses that IPV happens across economic strata and in all walks of life. “Every time I run this workshop, a medical student who comes from a very privileged background, from a very financially stable, loving home, comes to me, saying this is happening to her. It happens everywhere. I’ve got medical colleagues, several, who have experienced intimate partner violence. It doesn’t discriminate.”

Republished from Spotlight under a Creative Commons Licence.

Source: Spotlight

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Face to Face: “Fail your way to success”, Says Prof Behind Pioneering Drug Discovery Group at UCT

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Technical work on the discovery of new medicines is not commonly done in Africa, but Kelly Chibale, a professor in organic chemistry and founder of H3D at the University of Cape Town is changing this. PHOTO: Nasief Manie/Spotlight

By Biénne Huisman for Spotlight

Inside Professor Kelly Chibale’s office the bookshelves are packed with awards. On the walls, framed photographs include his class photo at Cambridge University in the United Kingdom, dated 1989.

Chibale is a professor of organic chemistry and founder of the pioneering Holistic Drug Discovery and Development Centre – H3D – at the University of Cape Town. While many important clinical trials have been conducted by Africans in Africa, the kind of drug discovery work that Chibale is doing is rare on the continent.

Chibale relays how he sees molecules everywhere – in hair, in clothes, in all of life around us. His animated voice fills the space as he speaks. “With organic chemistry, we are very visual. We look at chemical structures. If you give me a chemical structure, oh my goodness, my head starts racing about what I can do with it, or how I can change it to create new properties or new materials.”

H3D has 76 staff members investigating novel chemical compounds that could become new lifesaving medicines, with a focus on malaria, tuberculosis, and antibiotic-resistant microbial diseases.

Effectively a small biotech company embedded within the university, to date, H3D’s most notable discovery was a compound in 2012 which they named MMV390048, which had the potential to become a single-dose cure for malaria. Phase I clinical trials saw MMV390048 tested on human volunteers in South Africa and in Australia.

“In Australia, the testing model used is a volunteer infection study where human beings volunteer to be injected with the malaria parasite, which they know can be treated using available medicines,” says Chibale. “And then a section of those are given the experimental drug. And it worked beautifully there.”

‘Fail your way to success’

He adds, “People don’t realise this – there’s no medicine that will be given to people if it wasn’t tested on people first. Even me as an African. Oh man, I suffered from malaria as a child in Zambia many times. Thanks to our government then I’d be taken to a health facility and get malaria tablets, which I took and got well again. Otherwise, I would have died. Malaria kills very quickly. Now this is something I didn’t know then, something I took for granted. Only much later in life did I realise, goodness the medicine I took – someone somewhere invested in its research and development. And someone, somewhere, another human being, volunteered for that drug to be tested on them for my benefit.”

In 2017, the compound made it to Phase II clinical trials in patients with the disease, but further development was halted in 2020 when extensive further tests showed toxicity signals in rats – not rabbits though, Chibale says, adding that they had to err on the side of caution.

“In drug discovery, you have to kiss many frogs before you meet the prince,” he says. “Many drugs fail to progress. People focus on one product that makes it onto the market, right? But there are many failures that don’t even see the light of day. In this industry, you fail your way to success.”

H3D’s most notable discovery was a compound in 2012 which they named MMV390048, which had the potential to become a single-dose cure for malaria. PHOTO: Nasief Manie/Spotlight

Their work continues. In April last year at a function at Cape Town’s Vineyard Hotel, multinational pharmaceutical company Johnson & Johnson announced H3D as one of its three satellite centres for global health discovery. The other centres are in London and Singapore. At the time, Johnson & Johnson stated, “Driven by some of the leading researchers in Africa and discovery science, the satellite center [H3D] is focused on outpacing the rising threat of antimicrobial resistance by accelerating innovation against multidrug-resistance gram-negative bacteria.”

Seated at a boardroom table in his office, Chibale laughs deep from his belly. “We associate Johnson & Johnson with baby powder, but there’s much more…”

His left arm is in a sling following shoulder surgery – an injury stemming from lockdown when he slipped and fell while hiking on Table Mountain. “It happened just here, above the university,” he gestures, with his other arm.

Chibale and his wife Bertha live on the university’s campus, where he has served as warden of student residence Upper Campus Residence, formerly Smuts Hall, since 2015. Here he weathered the #rhodesmustfall and #feesmustfall protests, which saw students torch vehicles and police deploy stun grenades a stone’s throw away from his home.

Referring to his injured arm, he says at least his writing arm wasn’t hurt and that he can still type with one hand.

From a village in Zambia

Mentions of gratitude underpin the story of his journey, which starts in a village without electricity or running water in Zambia’s Mpika district. His father died when he was two months old. Laughing, he relays how hearing in his one ear is still impaired after being ambushed as a kid while stealing mangoes.

“This was a township,” he says. “So I’m climbing up a tree to steal mangoes and I was coming down. This gang, or well guys who were playful, had surrounded us. There were only about four of us, of who three managed to escape. And I was the only one left. Oh my goodness. And they took a big rock and smashed it to my ear. And then, when they saw me bleeding, they actually ran away. They were so scared of the damage they had done. Oh, that day! Anyway, so I went home and lied to my mother and said, no I went to school and tripped over a hole.”

During high school classes, thanks to an excellent teacher, he became fascinated with chemistry experiments. He went on to study organic chemistry at the University of Zambia, where he fell in love with the logical nature of organic molecules. “These things cannot be planned. I simply fell in love with organic chemistry, in the same way I fell in love with my wife Bertha,” he says.

From early on he realised education was a way out of poverty. “To get out of poverty, you either play sport or you follow education,” he says. “So I started applying for scholarships, writing letters to universities around the world. And I got rejected. I kept applying and kept on being rejected. But I didn’t give up. I kept applying.”

His first job was at Kafironda Explosives in the mining town Mufulira, on Zambia’s Copperbelt, where he made detonators, dynamite, and other explosives for use in Zambian mines. Laughing, he says this would come to haunt him later while applying for a visa to enter the United States. “There was a section on the form where you had to declare whether you’ve worked with explosives,” he says. “Of course, I said ‘yes’, and fortunately nothing happened.”

During two years at Kafironda, he continued applying for scholarships. “And I remember this,” he says. “It was January of 1989. I got a letter saying you have been shortlisted for a Cambridge Livingstone Trust Scholarship. Please present yourself for an interview on the 26th of January at the Anglo-American Corporation offices in Harare, Zimbabwe… So that was my first time out of Zambia. The first time to fly on an aeroplane.”

‘This was my turn’

Competition for the scholarship was tight, with shortlisted candidates from several African countries. “So in that year, there were six of us from Zambia, from different disciplines. I was the only scientist. And of course, I’d been failing all this time, getting rejected. But this was my turn. It was God’s appointed time for me. Actually, I was the only successful candidate.”

At Cambridge, without having completed an honours or master’s degree, Chibale enrolled for a PhD under the late organic chemist Professor Stuart Warren. “So Stuart, this amazing, incredible man, just gave me a chance. I mean there was such a gap between me and my colleagues who had all done their undergraduates at Cambridge. But in life, you can moan and complain about a disadvantage, or you can turn it into a challenge. I mean, the first three to six months were rough. Stuart would recommend to me that I sneak into first-year undergraduate classes to catch up. Stuart, he saw something in me that I didn’t even see in myself, and really gave me a chance.”

Chibale’s work at Warren’s lab, developing new synthetic methods for optically active molecules, helped secure his first post-doctoral position at the University of Liverpool, in the United Kingdom, after which he joined the Scripps Research Institute in La Jolla, California, funded through a Wellcome Trust International Prize Travelling Research Fellowship.

“That was another miracle,” he says. “I was eligible for this fellowship only because I had lived in England for three years, which was a minimum requirement. And the scholarship was so good, it even gave me an allowance for my family. I haven’t forgotten. It was 1 000 pounds per month. In those days, the pound was much stronger than the US dollar. So I went from rags to riches. In Liverpool, I was walking most of the time while in California, I actually had a car!”

Over the years, he was gaining insight into the pharmaceutical sector – the science but also the entrepreneurial side that pushes innovation, all the while longing to bring this knowledge to Africa. Peers suggested he consider South Africa, and particularly the University of Cape Town [UCT]. Around 1994, then UCT Department of Chemistry head, Professor James Bull actually made Chibale an offer to pursue postdoctoral research – which he declined. “Because I thought there was going to be a civil war in South Africa! I remember watching the release of Nelson Mandela on TV in England, quiet, just watching.”

Towards the end of 1995, inside a copy of the British scientific journal Nature, Chibale found an advertisement for a position as a lecturer in organic chemistry at UCT and applied. “It was a calling,” he says. The family moved to Cape Town.

Then in 2010 at UCT, with five post-doctoral staff, Chibale founded H3D. At the time his mentors included Dr Anthony Wood, former Pfizer senior vice-president, now head of GlaxoSmithKline’s Research and Development, who arranged for Chibale to have a four-month sabbatical with Pfizer in the United Kingdom to learn about the practicalities of innovative pharma. Thirteen years later, H3D has blossomed.

Chibale says he is a Christian as well as a soccer and boxing fan. His wife Bertha runs a Cape Town catering business called Hearts and Tarts. They have three sons.

As the interview draws to a close, he looks up at his 1989 Cambridge class photo. “You won’t believe it,” he says. “Last year I visited my college at Cambridge with my wife and second son and they pulled out a copy of my handwritten scholarship application letter, written to them from Zambia all those years back.”

This precious relic of Chibale’s journey is not in his office. He keeps it on his desk at home.

Republished from Spotlight under a Creative Commons 4.0 Licence.

Source: Spotlight

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UCT Scientists Pioneer Technique in Africa to Speed up Clinical Metagenomics

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By Tatjana Baleta

UCT Lab technician Fadheela Patel, pictured here preparing mastermix in the clean room

In a first for the African continent, researchers at the University of Cape Town are using a cutting-edge technique to fast-track the diagnosis of disease, ensuring patients receive the correct treatment sooner.

Clinical microbiologists Professor Adrian Brink and Dr Gert Marais at UCT’s Faculty of Health Sciences have operationalised clinical metagenomics in South Africa, transforming the procedure from a complex logistical procedure to a routine test.

Clinical metagenomics fast tracks the medical diagnostic process, cutting turnover time down – from sample to result – from weeks or even months to just a few days. It can also be used as a ‘sentinel surveillance tool’ to spot new infectious diseases and sound an early warning alarm for future pandemics.

“This kind of technology has never been used in South Africa and as far as we know, the African continent. “Certainly there’s no diagnostic lab in South Africa that does it,” says Brink. He and Marais believe they are the first to develop a clinical metagenomics service in Africa.

Clinical metagenomics is the detailed analysis of all the genetic material (DNA and RNA) in samples from patients – including that of the host (in this case, the patient), and of the microbes living within the host, like bacteria, viruses and fungi.

Gene sequencing everything but the kitchen sink

The genetic sequences appearing in a sample are compared to a database of all known organisms, allowing any and every pathogen present within the patient to be detected at the same time from just one sample. This metagenomic approach is sometimes referred to as “agnostic sequencing”.

Key steps in Brink and Marais’ clinical metagenomics study on the brain
1) A medical sample is obtained (from cerebral spinal fluid in their study) and treated to extract and purify all
the nucleic acids (genetic material) it contains. These DNA fragments are then made into a ‘library’ by
attaching short molecules called adaptors to the ends. This prepares the sample to be run through a
sequencing machine.
2) The genetic code of the library is read in real-time by running it through a sequencing machine. This
generates a series of ‘reads’ (DNA sequences).
3) The reads are compared to an online database of all known organisms’ genetic codes, allowing any and
every pathogen present within the patient’s brain to be detected at the same time from just one sample.
4) The results are examined for matches with infections organisms and used to determine appropriate patient
treatment.

By contrast, conventional diagnostic testing requires testing individually for a specific suspected disease. If the result comes back negative, a new sample will need to be taken and sent for a different test – a lengthy process when lives are at stake.

“In some cases we investigated, patients had a disease that could have been treated if it had been identified initially. But because the diagnosis could only be made months later, it was too late [to save them]. That’s where the idea for our study originated,” says Marais.

Brink recounts the case of a cancer patient who developed neurological symptoms. “Because he was highly immunocompromised, the list of potential causes for these symptoms was a page long,” says Brink.

The patient passed away, and clinical metagenomics testing of a sample taken at the autopsy revealed he was suffering from Aspergillus, an aggressive fungal infection that requires specific treatment.

Although he was already very sick due to cancer, Brink says the untreated central nervous system aspergillosis may have led to the patient’s death. “If clinical metagenomics methods had been available at the time, the right therapy could have been started weeks earlier, potentially changing the outcome for this patient,” he says.

Brink and Marias used clinical metagenomics to diagnose neurological disorders and study the effects of COVID-19 on the brain. It’s an area of health care where a timely diagnosis is particularly important. “Once the brain is damaged, there’s no going back,” says Marais. This research is currently under review for publication and expected to be released shortly.

While metagenomics has been applied in research settings in Africa before, this is the first time the method has been fully operationalised for clinical applications on the continent – meaning that all sample processing and analysis can now be done in the same laboratory in real time.

Previously, researchers in Africa have had to send samples overseas to Europe or the United States for processing. The reason: the chemical reagents required to run clinical metagenomic tests, despite in some instances being as easy to access in Europe as a DHL order, were not readily available in Africa.

Supported by funding from Oppenheimer Generations Research and Conservation, Brink and Marias remedied this by establishing a reagent supplier pipeline for South Africa, a tricky task when the pandemic had interrupted global supply chains. With a reliable source of reagents, samples can now be processed in labs in South Africa, opening the door for advances in medicine and research on the continent.

Building capacity instead of ‘helicopter research’

Marais emphasised their focus on upskilling and building capacity for Africa, in contrast to the ‘helicopter research’ that has defined clinical metagenomic work on the continent up to this point. “Our goal was to increase the capacity for infectious disease diagnostics going forward, rather than just coming in, testing a few samples, publishing a paper and leaving,” he says.

According to Marias, most prior metagenomics work in Africa has been in the form of discreet research projects with an international collaborator or as field work for an international lab, with little investment in local medical infrastructure and capabilities.

Their initial work so far has already created opportunities for skills transfer in genetic sequencing and bioinformatics at UCT medical school and medical research departments, and at institutes in Johannesburg.

Although the high cost of reagents and lack of standardised protocols remain challenges for a clinical metagenomics rollout in Africa, Brink and Marais are confident that the technology can become a cost-effective tool to improve patient individual care and to identify novel pathogens in low- and middle-income countries (LMICs).

A vast range of applications

Their new paper, co-authored with Associate Professor Diana Hardie and published in The Lancet Microbe in December 2022, calls for the expanded infrastructure developed in LMICs for COVID-19 monitoring to be leveraged to improve infectious disease diagnostics through clinical metagenomics.

“We applied clinical metagenomics to the COVID-19 brain, but the picture is bigger than that,” says Brink. Clinical metagenomics can be used for diagnosing an array of diseases across many health disciplines. In collaboration with colleagues at Cape Town’s Groote Schuur Hospital, Brink and Marias are now exploring the application of the technology in orthopaedics, neurosurgery, haematology-oncology and cardiothoracic surgery.

Specifically, they’re looking at patients with prosthetic joint infections, heart valve infections, brain tumours and leukaemia. The team welcomes collaborators and asks researchers and health care professionals across the continent interested in utilising clinical metagenomics to reach out to them.

Brink and Marias are also examining patients suffering from severe respiratory tract infections without a diagnosis, another area where clinical metagenomics is particularly revolutionary.

Because the genetic sequences found in patient samples are compared to a database of all known organisms, if a sequence yields no match to the database, there’s a chance it could be a novel pathogen.

Since its first reported clinical application in 2014, the technology has already supported the discovery of novel viruses, including identification of the original strain of SARS-CoV-2 (the virus that causes COVID-19) in Wuhan, China.

This application is particularly relevant in LMICs where novel pathogens pose a higher risk due to socioeconomic factors and a lack of infrastructure to deal with local outbreaks. However, despite this, infectious disease surveillance infrastructure is more developed and readily available in high income nations.

While hurdles remain to be navigated before clinical metagenomics can be widely accessible across Africa, the team is confident that technology holds real promise for advancing the continent’s capabilities for medical research and diagnosis. “There aren’t a lot of people doing this kind of thing [in Africa], but this is the future,” says Brink.

Source: University of Cape Town Faculty of Health Sciences