Testing Challenges With COVID-19: Why DNA Synthesis Is Critical.
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April 8, 2020

As the world struggles with the COVID-19 global pandemic, researchers, public health laboratories and diagnostics companies are working around the clock to understand the disease better and minimize its impact on society. Although a valiant effort, we are struggling to keep up with the speed at which the virus is spreading. One of the key challenges in the United States is that we initially relied on the Centers for Disease Control and Prevention to develop a diagnostic test and then had to rely on them for the reagents and protocols needed to run that test. Unfortunately, the original assay suffered from both design flaws and logistical challenges, creating a lag in the accessibility of vital diagnostic testing. This delayed our ability to understand and mitigate the spread of the disease. 

Are there technologies that could have helped buy us more time? Yes. Accessible, on-demand DNA synthesis could change the way we manage and cope with pandemics in the future.

What does DNA synthesis have to do with diagnostics? Isn’t reading or detecting the DNA of a virus much more important than writing DNA when battling a pandemic? It would be easy to think this as the advances in next-generation sequencing over the past decade have allowed us to understand the genetic make-up of this novel coronavirus more quickly than ever before. However, next-generation sequencing alone is insufficient to help stem the tide of a viral pandemic.

Sequencing of the SARS-CoV-2 genome back in early January was a critical first step in our development of countermeasures, providing scientists the blueprint they needed to begin developing diagnostics and therapeutics. Ongoing sequencing is giving further insights into how the virus genome changes over time and helps epidemiologists understand its spread and evolution. But sequencing cannot yet offer the speed, throughput, ease-of-use and price point to allow for population-based diagnostic testing. Other approaches, such as PCR — and, more recently, CRISPR-based methods — can do this; this is where access to custom DNA is vital.

Let’s focus on PCR-based methods. Real-time reverse transcription PCR (rRT-PCR) is a tried-and-tested, cost-effective, accessible and scalable technology. It has been used in diagnostics for many years and can be used with confidence to detect the presence of viral RNA in a human sample. Critical ingredients of any diagnostic rRT-PCR assay are the primers and probes designed to recognize a highly conserved region of the viral genome (one which does not mutate quickly) with high sensitivity, specificity and reproducibility.

Primers and probes are short, custom pieces of single-stranded DNA. Primers were named for their ability to prime the DNA sample in precisely the right location for the polymerase enzyme to bind and initiate copying of the targeted locus of the viral genome. Probes are fluorescently labeled pieces of DNA designed to bind downstream of one of the primers during the PCR and generate a fluorescent signal. This signal confirms that we are seeing only the virus we are looking for, allowing us to determine viral load accurately.

Designing the best primers and probes for an rRT-PCR test is not a trivial task. Computer algorithms provide a good starting point but often fail to predict how these pieces of DNA will behave in the actual test. Sometimes they don’t work at all. In other cases, they may cause non-specific amplification or other experimental artifacts — leading to a false positive or false-negative result. 

A benchtop, on-demand DNA synthesizer of the kind that DNA Script is developing would significantly speed up diagnostic test development during time-critical situations. It would have allowed the CDC to not only print the primers and probes in mere hours but would have enabled them to test hundreds of combinations in a matter of days. They would not have had to wait on older-generation chemical synthesis (performed by only a few manufacturers) and multiple cycles of shipment from those sites — however expedited — to learn which primer and probe combinations did and didn’t work. Furthermore, when they realized that their original design had limitations, on-demand synthesis would have enabled them to correct the design flaw and deliver new kits sooner.

The potential benefits of in-house DNA synthesis go even further. Primers and probes would not have to be produced by centralized facilities and distributed over long distances and across borders to test sites. Test developers could simply share the sequences with accredited sites, who would be able to print the primers and probes themselves, over and over again, on-demand, for as many tests as needed. The distributable nature of this technology provides different geographic regions around the world equal, rapid access to the capability and reagents required to develop and implement their own testing. As the current COVID-19 global pandemic illustrates, a delay of even one day has profound consequences. Ultimately, decentralized access to on-demand DNA synthesis could change current paradigms of diagnostic development and manufacturing. No waiting for FedEx or customs. No running out of urgently needed tests. Imagine that.

To learn more about DNA Script’s EDS system and how it could enable your research please email us at contact@dnascript.com.