An all-hands-on-deck response to the COVID-19 pandemic is helping accelerate the maturity of promising molecular diagnostics technologies.
In the wake of the COVID-19 pandemic, scientists and healthcare professionals around the world dropped everything and rallied together around a single cause.
Governments quickly stepped up with financial support to fuel this international pandemic collaboration. Innovations in treatment and outbreak control were fast-tracked as a result – providing us with valuable tools that are proving crucial in the fight against a global health crisis.
Take the COVID-19 vaccines developed by Pfizer and Moderna. Vaccine development is traditionally a complex, tedious process that can last up to 10-15 years; but thanks to these synergistic efforts, they were granted Emergency Use Authorization (EUA) in the United States in less than one year.
The scientific community’s commitment offers a glimmer of hope in an otherwise devastating situation and will undoubtedly continue as we look to transition towards a post-pandemic world. One area in particular that will require further advancement is traditional COVID-19 testing, which we covered in this March 2021 article.
From the financial and collaborative efforts during the pandemic, what other diagnostic and genomic innovations can we expect from the pandemic-related research to produce over the short-term future? Read on for a few that we’re keeping a keen eye on.
Multiplex PCR Testing
Polymerase Chain Reaction (PCR) testing has been relied upon heavily throughout the pandemic thanks to its high level of accuracy in determining if an individual is presently infected with SARS-CoV-2. Scientists are working very hard to optimize the PCR workflow in order to shorten the turnaround time to generate the results, which is PCR testing’s one main deficiency.
Multiplex PCR testing takes workflow optimization to another level. With this technology, PCR is used to amplify several different sequences simultaneously. Multiplexing has been around for some time and has been helpful in combining multiple gene targets in one reaction to increase SARS-CoV-2 testing throughput.
Scientists are currently building on this concept through the development of multiplex iterations that can actually detect multiple different types of virus. Thermo Fisher (Multiple Companies, if we do not want to specifically call out Thermo), for example, is (if multiple use are)poised to release a single assay covering 4 different respiratory virus targets ahead of the upcoming Flu season – Flu A, Flu B, RSV, and SARS-CoV-2.
Limiting the Laboratory use of this technology would be the requirement for a PCR machine to have a minimum of 4 color multiplexing capability, 5-color multiplexing if an Internal Control is used, which could be a barrier for some laboratories. But nonetheless, many scientists, including Carl Hilliker, PhD of Thomas Scientific, believe multiplex tests will capture a significant portion of the market. “I believe we’re looking at next year’s COVID-19 testing iteration,” Hilliker said. “Labs will be able to test for multiple SARS-CoV-2 variants (and the flu) in one test, which will allow proper patient diagnosis.
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Variant Analysis and Next Generation Sequencing
Speaking of variants, chances are you’ve heard quite a bit about them in the news. Multiple SARS-CoV-2 mutations have sprung up in many corners of the world – including South Africa, Brazil, the United Kingdom, India and even the USA (California & New York Variants). Each Variant has been reported to vary in terms of transmissibility, virulence, and antigenicity.
These contrasting characteristics present challenges for pharmaceutical companies, as certain vaccines and antivirals may render ineffective with certain variants. This will undoubtedly continue to be a hot button issue as more variants are likely to emerge.
Next Gen Sequencing, or NGS, is proving to be a crucial weapon in our battle against SARS-CoV-2 variants. NGS has transformed genomic research with its ability to study biological systems in more detail and at a larger scale than ever before. The technology utilizes parallelized platforms to achieve ultra-high throughput – up to 43 billion short reads per instrument run – allowing labs to tackle increasingly complex research questions with great efficiency.
Some large health system labs, like the Mayo Clinic’s Division of Clinical Microbiology, are already relying heavily on variant sequencing for surveillance. Top health agencies have even jumped on board, with the WHO recently advising that, where feasible, countries should "increase routine systematic sequencing of SARS-CoV-2 viruses to better understand SARS-CoV-2 transmission and to monitor for the emergence of variants." The CDC is also gaining traction for a $2 billion NGS-based program called “Advanced Molecular Detection”.
The promise of NGS, however, goes far beyond COVID-19. Its ability to rapidly sequence entire genomes – and deeply sequence targeted regions – is also helping researchers better understand DNA-protein interactions, uncover mysteries of the human microbiome, identify novel pathogens, study new cancer biomarkers, and more. We have really only scratched the surface of NGS’s potential.
Check back for future NGS product offerings.
Non-Invasive Prenatal Testing
One additional testing area that has been evolving over the last few years is Non-Invasive Prenatal Testing (NIPT), a method that analyzes Fetal DNA fragments from a pregnant woman’s blood to determine genetic abnormality risk of the fetus.
The successes scientists have achieved over the last few years has helped pave the way for NIPT advances – some of which are substitutes for risky invasive tests. Companies like Arcedi Biotech are rolling out tests that rely on detecting rare fetal cells in maternal blood, rather than alternatives that may result in miscarriage.
Arcedi’s test (and other similar products) labels fetal DNA with a fluorescent tag and hybridizes it using 4x180K microarrays for eventual detection on a scanning confocal microscope. Rather than extracting DNA from the maternal sample– which could result in contamination from maternal/fetal DNA mixing – this process instead captures the desired Fetal cells, separates them from the Maternal cells and allows a pure Fetal DNA sample, free from contaminating Maternal DNA, which allows for testing to be done specifically on the Fetal material, providing opportunity to perform Fetal specific testing.
Over the years to come, NGS technology is poised to improve NIPT capabilities further, resulting in even deeper research and an even safer testing environment. Continued progress is likely to result in NIPT becoming the accepted testing methodology for an increasing number of abnormalities and conditions, as well as obtaining expanded insurance coverage.
Thomas Scientific’s Molecular Diagnostics experts can help your lab create its own custom NIPT workflow, including hybrid DNA capture. Click here to receive a free consultation.
Breathalyzer technology is also being leveraged as a diagnostic tool for SARS-CoV-2. Companies and organizations around the world are developing products that work much like traditional blood alcohol content detecting devices – delivering results on a possible infection with over 90% accuracy.
COVID-19 breathalyzers detect cellular biproducts in exhaled breath and can deliver results in as little as 3 minutes. This makes them ideal for use at large events or gatherings, especially those in an open air atmosphere. The British Columbia Cancer Research Centre (BCCRC), for example, developed a technology to detect Lung Cancer that has been adapted to be utilized to detect COVID-19, and will be adminsitered at the annual Canadian International Dragon Boat Festival this summer.
Successful deployment of the BCCRC product will undoubtedly lead to wider use cases of COVID-19 breathalyzer technology as we transition back to normalcy. That said, continuous refining will need to be done as we learn more about variants and their characteristics. Antibodies against one variant does not necessarily mean the same level of antibodies for another, and vice versa.
Nevertheless, there is optimism that this same breathalyzer technology could be applied to other pathogens and conditions going forward. Scientists will continue to apply this, and other lessons learned from the COVID-19 pandemic towards a safer, more prepared future.