Outrunning viruses with molecular tools

Dr. Allison Glass likes to get her heart racing. Years before she became a clinical virologist in Johannesburg, her hometown, Dr. Glass worked as a neurosurgical medical officer in emergency medicine in a rural hospital. “One of the things I enjoyed about working in an emergency department was the adrenaline rush and the sort of immediate need to respond to a situation and stabilize the situation,” she recalls. ‘I've always sort of felt a bit like a fixer, where a problem comes along and you need to rush to solve it, to stabilize the patient.” 

Every morning before she goes to work, she gets her blood pumping with a serious run, putting in 40–60 kilometers a week. But nothing really gets her heart - or her mind - racing like viruses. “Each virus has its own little characteristics, its own personality, almost, with how it causes infections. Such small little particles that can't even carry out a lifecycle on their own, and that are dependent on other organisms to be able to survive, can cause such devastation,” she says.

Glass is a clinical virologist and head of molecular pathology at Lancet Laboratories, a private pathology practice with locations across South Africa and in 10 other African countries. Lancet Laboratories offers both specialized services and routine diagnostics from both its main central laboratory in Johannesburg - which Glass runs - as well as about 200 hospital laboratories and depots throughout the country. 

In some ways, the laboratory reminds her of the emergency room. “There’s this pressure to try and get a result out to help the doctor identify what's going on with his or her patient.” And having worked both at the bedside and at the bench, Glass understands just how vital it is to provide those answers as fast as possible. “We’re able to give the doctors their results so that they can manage their patients quickly and effectively.”

The first to detect Omicron

Glass’s home country suddenly found itself in the center of the ongoing COVID-19 pandemic at the end of 2021. Two SARS-CoV-2 variants were discovered in South Africa: Beta and Omicron. The latter was identified for the first time in Lancet Laboratories in Pretoria in early November 2021 by a junior scientist who noticed an S gene dropout in a sample. The same dropout then appeared in samples in Johannesburg. At the same time, the SARS-CoV-2 positivity rate shot up dramatically, from 3% to 16%.

“We sequenced some of these samples and found that we were dealing with a variant that hadn't been described previously. Why it was identified as a variant of concern almost immediately is because of the large number of mutations in the spike protein area, which raised concerns around transmissibility.” They reported their results to South Africa’s National Institute for Communicable Diseases, which soon alerted the world.

With cases and hospitalizations rising, high throughput became essential. “We obviously were under pressure to get out the urgent results as quickly as possible,” Glass recalls. “The QIAstat-Dx offered us the advantage of being able to give the doctor a quick COVID result by running the respiratory panel onsite at the hospital. So we can prioritize the very urgent patients on those platforms while we send the large bulk of routine work through to the main lab for processing on our routine platforms.”

Moving closer to the patient

While Lancet Laboratories has been using QIAGEN products for many years, the company acquired its first QIAstat-Dx syndromic testing platform in early 2020 and has since placed platforms in 12 hospital labs. “We're of the opinion that molecular testing, especially for infectious diseases, needs to move closer to the patient,” Glass says.

The QIAstat-Dx allows them to handle more samples locally and immediately without batching or sending them to the main Johannesburg lab. “It cuts our turnaround time down by at least 12 hours,” she says. “Doctors are immediately able to get those results and act on them, which has a good benefit for the hospital with regards to infection control, but also guides treatment decisions around antivirals and antibacterials.”

The respiratory virus panel and gastrointestinal panel have been two of their most relied-on syndromic testing panels, she says. “Syndromic testing is really important because multiple different bacteria and viruses might cause exactly the same symptoms. From an infection-control point of view, and a treatment point of view, it's really important to know what is causing the infection. Without that knowledge, a patient may have to undergo a lot of testing, remain in the hospital longer and may be given unnecessary treatments. All of that negatively impacts on the outcome for the patient—and also increases the cost of care,” she says.

Because the QIAstat-Dx automates so much of the process, it limits human error and potential exposure to pathogens, and is accessible to technicians with good basic lab practices, she says. “They don't need to be specifically molecular trained to be able to use this platform. In a country where molecularly trained staff are not always readily available, this is a really handy and very useful way to get molecular testing spread out across the country.”

Evolution of pathology testing

South Africa faces infectious disease challenges beyond COVID-19, most notably hepatitis, tuberculosis and HIV. “Molecular testing is such an important area of evolution in pathology and laboratory testing, but one of the unfortunate aspects is, as with any new type of technologies, that often the cost is high, and that contributes to a widening gap between the haves and the have-nots,” Glass admits.

But the pandemic may have moved the needle. “Fortunately, to some extent, COVID-19 has contributed to a ramping up in production of molecular testing capabilities and capacity, and that does help to bring costs down,” she notes. “It is really my hope that in the next few years, the cost of molecular testing will come down further so that it is more accessible to a broader range of people.”

Until then, she’ll keep her heart rate up in the lab and in the races. “I do sometimes still miss the action of a busy casualty department,” she admits, “but I’ve enjoyed my time in the laboratory and the challenges that come with running a busy lab.”