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Diagnosing disease in your DNA

- Deborah Minors

Molecular diagnostics uses genetic material to look for infectious organisms like TB and HIV. If you don’t know what you’ve got, how do you treat it?

Wits alumnae Professor Wendy Stevens and Professor Lesley Scott delivered the 13th Prestigious Research Lecture in the Faculty of Health Sciences at Wits on 14 June 2016. Their lecture was entitled: “Unlocking access to Global HIV and TB care through Molecular Diagnostics”.

What lurks within?

 Stevens and Scott head a team of predominantly women scientists who have dedicated 15 years to finding ways to diagnose South Africa’s leading infectious disease killers: HIV and TB. Through their efforts, South Africa is one of the first countries worldwide to embrace molecular diagnostics at scale.

Molecular diagnostics is becoming fundamental to medical diagnosis. If you don’t know what you’ve got, how do you treat it?” says Stevens, who is Head of the Department of Molecular Medicine and Haematology at Wits University and the National Health Laboratory Service (NHLS).

The implementation of molecular diagnostic technology by Stevens and Scott, and their teams at Wits and the NHLS, is revolutionising HIV and TB diagnosis in South Africa.

Tech to terminate TB infection

Scott, Associate Professor in the Department of Molecular Medicine and Haematology at Wits and Head of Research and Development for the National Priority Programmes of the NHLS, says, “South Africa is the epicentre of TB and HIV. If we can’t treat it here, we can’t treat it anywhere. In China, they want to use similar molecular technologies and approaches to diagnosing TB.”

The technology that Stevens and Scott have implemented for TB diagnosis specifically is called the GeneXpert. It’s a simple test that uses a patient’s genetic material (DNA, RNA) to show within hours if a patient has TB. Previously, this diagnosis took six weeks.

The GeneXpert ‘reads’ the genetic material and amplifies the TB bacteria. Then an SMS or WhatsApp message can be sent to the healthcare worker or patient that says ‘yes’ or ‘no’ to the presence of TB, and whether or not the patient is drug resistant.

“The GeneXpert can immediately identify over 80 percent of individuals with multi-drug resistant TB, which is highly infectious and 60 percent fatal,” says Stevens. “The quick turnaround for results means that patients don’t go missing or infect others or die. In 2014 approximately 9.6- million people developed TB globally and 1.5 million died.”

TB diagnosis using the GeneXpert machine can now be done at the patient’s bedside, irrespective of whether they are in a rural clinic or city hospital.  However, the machines must be checked prior to testing to ensure their efficacy. Initially this was almost impossible to do.

“Not only would it take several weeks but it also posed a severe biosafety risk, because it meant transporting live organisms, sometimes over great distances,” explains Scott.

Scott and her R&D team subsequently invented the Smartspot TBcheck, which checks the efficacy of the GeneXpert machine on the spot before a patient is tested. Scott won the 2015 Innovation Prize for Africa and the Special Prize for Social Impact for the Smartspot TBcheck. This technology saved an estimated 37-million lives between 2000 and 2013 and the World Health Organisation has approved it.

“Leap-frog” technology

Other molecular diagnostic tools, for HIV for example, will WhatsApp or SMS a number that shows a patient’s viral load (the quantity of HIV virus in the blood). No virus in the blood means the patient is doing well. Testing the viral load is the only way to establish if a patient is not taking their medicine or is resistant to antiretroviral treatment (ARV).

“Drug resistance is the next big thing in molecular diagnostics across all infections,” says Scott. “Multi-drug resistant TB is way scarier than Ebola.”

Molecular technology enables the rapid communication of test results to the patient and healthcare worker, and to a national centralised data warehouse. The quicker infected patients are informed and treated, the less likely the chance of transmission, which means fewer HIV and TB-related infections and deaths. It’s revolutionary technology in a country like South Africa where the TB-infected population has up to 65 percent co-infection with HIV.  

“It’s an example of ‘leap-frogging’ – using technology to solve primary healthcare problems,” says Stevens. “South Africans are particularly innovative because we have a lot to fix, and Wits Medical School graduates specifically are equipped with skills because of this need. We’re applied scientists with a generalist approach, so we can address needs at scale.”

Taking TB tech to scale

Together with the National Department of Health, the NHLS, and clinical stakeholders, Stevens put together the plans for the use of several molecular technologies in South Africa – the first country to roll these out at scale.

Molecular diagnostics enables the collection of large volumes of test results in a central data warehouse in real time that can be fast-tracked to the clinics – volumes such as four-million HIV viral loads, four-million CD4 counts, and two-million TB tests in 2014. In South Africa, molecular diagnostics has contributed to a reduction in HIV early infant diagnosis from 25 percent in 2006 to less than 2 percent today.

Stevens says molecular diagnostics can also help healthcare workers manage the load of patient care. Nurses and other healthcare workers who may be ill-equipped in rural South Africa can easily use the tech to simplify and catalyze testing and results. “It’s about getting the right test to the right patient at the right time.”

A South African solution

“We tailored the diagnostic tests for South Africa, and they reach 80 percent of the public sector. Test results go to 266 laboratories across the country. South Africa is unique in that the NHLS is entirely networked,” says Scott.

“With molecular technologies we can now implement highly centralised, high throughput testing, as well as decentralised, low throughput testing in clinics and hospitals countrywide. This considerably reduces the money spent on these tests while simultaneously advancing, faster, simpler, more accurate testing and diagnostics in future – potentially for any kind of disease.”

Precision medicine ahead

Molecular diagnostics has potential in non-communicable diseases too.  Here ‘precision medicine’ refers to the use of molecular testing on the DNA/RNA of patients with cancers and inherited disorders, and in evaluating your likelihood of infection. For example, precision medicine can find the gene in a woman’s DNA that causes breast cancer, predict the outcome, and select the right treatment. The doom of diagnosis aside, it empowers that woman to make informed choices.

“The medicine of tomorrow is personalised. In future your DNA will be in the pharmacies,” says Scott. “The laboratory is the back-bone of getting a result. The ‘back-room girls’ in the lab will be coming to the fore once we realise what this tech can do.”

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