hospital, patients, covid-19, medical staff
Infectious Disease | QIAstat-Dx

Outrunning viruses with molecular tools

March 14, 2022

All local recommended safety guidelines followed at the time of interview.

During the last gasp of 2021, Lancet Laboratories in South Africa made a startling discovery - the new SARS-CoV-2 variant Omicron, which soon gained worldwide attention. Dr. Allison Glass, clinical virologist at Lancet Laboratories, is dedicated to outpacing viruses and she thrives on fast results, whether she’s running an ultramarathon or running a state-of-the-art molecular testing lab. But what is most fascinating to her, are the multitude of viruses out there and how an entity that can’t even carry out a life cycle on its own can cause so much destruction.

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.”

When viruses hijack our cells, they can cause issues as mild as a sneeze from the common cold or as devastating as blood cell rupture from Ebola - a disease that drew Glass towards virology when she first read about it. “It’s our trying to understand how to live with them, minimize their impact on us, and understand how our bodies react to them that I've always found so fascinating,” she says. In her current role as clinical virologist at Lancet Laboratories, identifying viruses is key to appropriate patient care. And she explains how the QIAstat-Dx has helped speed up various diagnoses.
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What fascinates me about viruses is the diversity of viruses out there and the diseases that they cause… that such small little particles that can't even carry out a lifecycle on their own can cause such devastation.
Dr. Allison Glass, Clinical virologist, Lancet Laboratories, Johannesburg

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.”

Allison Glass, lab
Dr. Allison Glass has now been at Lancet Laboratories for 11 years. In her first role as a clinical virologist, she closely consulted with doctors on patient results. When she became head of the molecular pathology lab, she expanded her knowledge to include oncology and genetics. Her team processes some 3,700 tests for infectious diseases, oncogenetics, genetic diseases, paternity testing and a variety of others. “A routine day would be coming into the lab and assessing what work there is for the day, responding to doctor's phone calls and queries, how to understand or interpret the results they've received and how to manage their patients further based on our results.”
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With diseases like respiratory tract infections and meningitis, multiple different bacteria and viruses might cause exactly the same symptoms.
Dr. Allison Glass, Clinical virologist, Lancet Laboratories, Johannesburg

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.”

scientist, lab
When Glass was still at medical school, her sister was a librarian working at the medical library. “Which was very useful because she would get all the new books for me before anybody else,” Glass recalls. A popular non-fiction thriller planted the first seeds for her future career in virology: Richard Preston’s The Hot Zone, a dramatized account of the discovery of Ebola. “I thoroughly enjoyed it,” she says. “I thought that it was so exciting, reading about this challenging virus and the scary disease it causes and the work that the scientists did to understand it.”
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With a syndromic approach, we test for multiple bacteria and viruses simultaneously. So we can give the doctor a very quick answer so he knows immediately what he's dealing with.
Dr. Allison Glass, Clinical virologist, Lancet Laboratories, Johannesburg

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.”

Allison Glass, lab, testing
“Some of the really good experiences we've had with syndromic testing is being able to treat patients with certain infections that might not have been expected,” explains Glass. “So for example, with cerebral spinal fluid testing in a community where we see a lot of HIV infection, we identify a lot of Varicella zoster virus, which can cause meningitis, vasculitis and conditions like that. These conditions were never appropriately diagnosed before, and there is appropriate treatment for them—an antiviral which can cause a dramatic improvement in a patient's condition very quickly.”
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