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Diagnostics Biochemistry and molecular biology, COVID-19, Microbiology and immunology, Clinical care

A Perfect Molecular Match

Few of us these days can say we’re unfamiliar with the threat of a pandemic – or the long tail of recovery after one. But how can we use emerging technologies to stay ahead of that threat? Molecular diagnostics offer us an opportunity to monitor populations, quickly identify and address infectious diseases, and even distinguish between multiple illnesses with similar or nonspecific symptoms. To take full advantage of these tests’ capabilities, we need to ensure that all people have equitable access to them – and we need to establish a pandemic preparedness infrastructure that allows us to act quickly on the information they provide.

Our pathogenic future

Pandemics are nothing new – but, with four influenza pandemics in the last 100 years, the regularity of such events is of great concern. The swift response to COVID-19 – particularly with respect to the development of diagnostics and vaccines – prevented a much worse outcome, but there have been more lethal and contagious pandemics in the past and preparation for the next one is really key to future success.

Simultaneous disease outbreaks in different areas of the world are to be expected due to our increasingly globalized economy, air travel, and increased opportunities for zoonotic transmission of pathogens to humans. That’s why it’s paramount to not only maintain global surveillance, but also invest in an infrastructure for a global pandemic preparedness system that nurtures research and capabilities in this area so that, when the next outbreak arises, our responses are swift and coordinated.

One way to do this in the fight against viral pathogens is to screen for common viruses with similar symptoms using so-called “syndromic tests” (so-called because symptoms that consistently occur together, forming a diagnostic entity, are called syndromes). Available syndromic tests enable the qualitative detection of multiple viruses at once – allowing pathology laboratories to distinguish between SARS-CoV-2, influenza, and respiratory syncytial virus (RSV) infections despite their similar symptoms. Although vaccination is key to reduce the spread of these pathogens and to prevent severe disease, syndromic testing is also valuable for rapid diagnosis, so that those with active infections can be isolated quickly to prevent further spread and receive appropriate treatment for the specific virus faster.

Diagnostics takes center stage

Diagnostic professionals are at the forefront of testing and diagnosing infected patients – so it’s important that they are consulted in the choice and implementation of diagnostic tests to ensure the best possible outcome for patients. When deciding on the type of test to use, several factors are at play, including the stage of the outbreak, the resources required, and the laboratory workflow in operation. During peak respiratory disease season, running single-target tests may result in a difficult-to-manage workload. Switching to syndromic testing, which combines multiple targets into a single test, can reduce overall workload and enable faster reporting – speeding up measures such as isolation and treatment.

Molecular diagnostics play an important part in the prevention and early response to outbreaks from many angles: identifying infected individuals, understanding community levels of immunity, and also monitoring the evolution of variants so that appropriately targeted vaccines can be developed. When designing diagnostic tests, it is vital to avoid viral genes prone to mutation so that infected cases are not missed. A rigorous process of research and development identifies optimal target regions that are then bioinformatically analyzed using primer design algorithms to select appropriate sequences. Following this, the sequences are tested to ensure the best possible sensitivity and specificity performance metrics are achieved by adjusting cycling parameters so that precise results can be obtained within an acceptable turnaround time.

Applying molecular tests

Molecular diagnostics are an extremely valuable tool when used correctly in the presence of appropriate clinical symptoms. They offer specificity and sensitivity with ease of use and interpretation, whether that’s through a single-target assay or a syndromic panel in a diagnostically challenging situation. However, their value is maximized when each test’s advantages and limitations are understood, so that the right test is used in the right circumstances.

PCR-based assays are still considered the gold standard in infectious disease diagnostics because they use common laboratory equipment and tolerate a wide range of input sample types. With the recent mpox outbreak and the constant threat of new and emerging viruses, broader syndromic tests are an excellent tool for building a global pandemic surveillance strategy.

PCR-based tests allow for high sensitivity and specificity. They use equipment already present in most labs and results can be obtained from a noninvasive nasal, nasopharyngeal, or saliva sample. Such workflows lend themselves to mass community testing because, with the addition of laboratory automation, throughput can be increased considerably. Modular, scalable extraction and liquid handling platforms allow labs to respond to surges in demand by removing bottlenecks such as sample accessioning and reformatting primary sample tubes into workflow-compatible consumables. At the same time, these platforms allow for full traceability of the sample to the patient result, thereby improving turnaround time.

But not all diagnostic settings are equal. PCR obviously involves the use of laboratory equipment, lab space, and sample collection logistics. Although it can be deployed to remote or underserved settings using mobile labs, that’s an expensive undertaking – and the workflow takes time to run. Increasing the speed with rapid extraction and PCR protocols results in less time to result, but also less sensitivity, so this needs to be balanced to mitigate the likelihood of false negative results. Rapid point-of-care testing in the form of lateral flow tests, for example, offers speed and convenience without requiring laboratory equipment, but these types of tests have a wide range of sensitivity and specificity and are generally most appropriate during the acute phase of infection. If patients are tested too early or too late, their results may not be reliable even with a high-quality rapid test.

I believe that molecular testing will become increasingly syndromic. Pathogens that present with similar symptoms will be tested for in a single panel or as a combined, multiplexed, one-tube test. Though single-target assays offer speed and sensitivity, the clinician needs to know what pathogen(s) they are looking for to ensure success. In the future, syndromic tests and panels will include a wider array of target pathogens – and I anticipate that we will see faster testing and ever more streamlined workflows.

What’s next?

With the changes in our climate becoming more apparent every year, vector-borne diseases are of great concern. Increasingly warmer and wetter weather supports the life cycles of mosquitoes and ticks, which can carry diseases between infected and uninfected animals – including humans. Such diseases include Zika, Chikungunya, yellow fever, malaria, dengue, and many others. In fact, the World Health Organization recognizes eight neglected vector-borne diseases that pose a huge burden of morbidity and mortality worldwide (1). Surveillance and early diagnostic testing are vital to effectively manage infected people and curb the spread of disease – and molecular testing approaches are key to catching the emergence of any novel pathogens.

Molecular diagnostics for routine testing and surveillance are a powerful armory against outbreaks of known pathogens and in the detection of new and emerging threats. Yet their success on the global stage is dependent upon partnership and collaboration within and between countries. We need adequate funding and resources to develop and distribute molecular tests – and, alongside that testing, we need collaborative, cross-functional research to create pandemic preparedness networks that will endure into the future.

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  1. WHO, “Vector-borne diseases” (2020). Available at:
About the Author
Anona Bamford

Regional Segment Leader, Applied Genomics at PerkinElmer, EMEAI.

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