The world is talking about the coronavirus pandemic and global health crisis we find ourselves living in. Healthcare professionals and researchers are scrambling for solutions to diagnose and treat COVID-19 patients and to slow the spread. Our medical systems and economies have been challenged in unprecedented ways. In a recent episode of our podcast Molecules, Microbes, and Multiomics, we hosted two of DNA Genotek’s R&D specialists Dr. Tara Crawford Parks and Jessica Wong, as well as our Microbiome Product Manager, Laura Cunningham. We discussed important challenges and solutions associated with global shortages of COVID testing supplies as well as the need for accurate and reliable results. I have highlighted the key topics discussed in the episode. If you would like to listen to the podcast in its entirety, you can click on the embedded link below.
One of the most important steps of any test focusing on infectious disease diagnostic testing is the biological collection process. Laura began the podcast episode discussing the challenges we are currently facing when it comes to collecting samples for COVID-19 testing and detection.
“I would say one of the biggest challenges for clinicians early on, and to be honest still, is reliable access to a constant supply of inventory. Swab companies couldn’t and still can’t manufacture enough swabs at a fast-enough rate to meet the testing demands.
There is also the consideration of safety for both the patient providing the sample and the healthcare professional conducting the sample collection. For example, nasopharyngeal swabs have been known to cause patients to sneeze and cough, which is one-way viral transmission puts medical staff at risk of contracting the disease. Not to mention, a healthcare professional must perform the sample collection resulting in over burdening our hospitals and clinics.” - Laura Cunningham
When testing first started for COVID-19, samples were collected using nasopharyngeal swabs. However, another sample type has emerged within the COVID-19 testing space and is currently being used in many testing facilities. Saliva as an additional sample type, and DNA Genotek’s specialty, is considered a suitable alternative for COVID-19 collection.
“Several studies published now support saliva as an alternative sample type to nasopharyngeal swabs to help facilitate the needed expansion of COVID-19 testing. We have two saliva devices, OMNIgene®•ORAL and ORAcollect•RNA, that are well positioned to support COVID-19 diagnostic efforts. These devices are designed for at-home collection, so participants can collect in the comfort of their own home, on their own time and do not have to wait in long line ups to get tested. Our products are safe and easy-to-use, have been proven to inactivate greater than 99% of the virus  , and have been validated extensively by us internally as well as, by third parties. In addition, there are several Emergency Use Authorizations (EUAs)   granted by the Food and Drug Administration using DNA Genotek’s devices.” - Laura Cunningham
After collection, the samples need to be transported to the lab where they will be processed. Sometimes it is overlooked just how important this step is in ensuring the stability of the collected samples. Tara explained how stability issues can arise during transportation from the collection site to the processing lab.
“Although the molecular detection methods used for viral testing do not require competent virus, there is an essential need for the preservation of nucleic acids in the sample. As Laura mentioned, there are supply shortages with swabs, the same issue is present for the availability of Viral Transport Media or (VTM) that the swabs are often inserted into following a collection. This acute shortage of VTM is contributing to delays in diagnosis and rationing of diagnostic testing. In addition, many of the VTM being used contain factors that can impair or prevent the detection of SARS-CoV-2 viral RNA by nucleic acid-based methods such as RT-qPCR. In addition to the issues surrounding stability of nucleic acids in certain VTM’s, the length of time that viral nucleic acids are stable also present challenges, particularly in areas where there are backlogs in testing laboratories. For example, there could be false negative results when there are delays in processing unstabilized samples.” - Tara Crawford Parks
Using our OMNIgene®•ORAL or ORAcollect•RNA collection devices containing stabilization chemistries overcomes these challenges by preserving nucleic acids present in a collected saliva sample.
“We have validated these products specifically for SARS-CoV-2 RNA stability during room temperature storage and during transport conditions. In addition, these samples are consumer safe (I.e. contain no guanidinium) and are validated for at home collections thus eliminating the requirement of a health care professional to administer the collection.” - Tara Crawford Parks
Jessica then continued the discussion by addressing important considerations and potential speed bumps for COVID-19 sample processing. The global demand for COVID-19 testing resulted in shortages of swabs and viral transport media. Jessica explained how there were also shortages of viral RNA extraction kits, which are necessary for preparing collected samples for downstream testing.
“The impact of these shortages is a backlog of samples waiting to be tested and a delay in diagnosis. When these standard viral RNA extraction kits are available, the extractions can take a couple of hours to perform, limiting the number of samples that can be processed in a day. These extraction kits are also costly and sometimes require specialized instruments for high-throughput processing.” - Jessica Wong
To overcome these challenges, DNA Genotek came up with an alternative sample preparation reagent and associated protocol: prepIT·Q2A
“prepIT•Q2A is a liquid based nucleic acid preparation reagent that’s designed to clean up saliva samples collected in OMNIgene®•ORAL and ORAcollect•RNA devices. Sample processing is quick, taking 5 min of hands on time and 30 min total time to get the sample ready for a downstream assay. It serves as a quick alternative to standard extraction methods and supports a direct-to-assay workflow. The protocol is also compatible with automated liquid handlers, which helps address the high throughput needs for COVID-19 testing.” - Jessica Wong.
Choice of technique for analysis
The next step in the sample collection to processing workflow is analysis. Tara and Jessica explained how the choice of technique for this step is important when analyzing COVID-19 samples. They discussed how common methods for analyzing samples in the context of SARS-CoV-2 include RT-qPCR and Next-Generation Sequencing (NGS) technologies. RT-qPCR is a fast and a relatively affordable way of screening samples for the presence or absence of SARS-CoV-2, so when quick population screening is required for a simple “yes or no” answer, RT-qPCR makes sense.
“In addition, there are several multiplexed RT-qPCR solutions that offer rapid detection of several respiratory viral pathogens simultaneously from a single sample. This approach reduces the reagents required for sample processing and provides an efficient means for surveillance of other common respiratory viruses such as Influenza and RSV, in parallel to SARS-CoV-2.” - Tara Crawford Parks
NGS can be used for sensitive detection of SARS-CoV-2. It provides a more in-depth look at viral sequences within the sample, allowing for genomic epidemiological tracking if samples are analyzed on a wider scale.
“We’ve worked closely in collaboration with other groups to demonstrate the compatibility of our collection devices, OMNIgene®•ORAL and ORAcollect•RNA, with RT-qPCR based viral detection assays, resulting in a number of EUAs granted by the FDA. We also have ongoing work to evaluate the performance of our collection devices with NGS assays. Collectively, this showcases our saliva stabilization devices across a variety of use cases in support of the global pandemic efforts.” Jessica Wong
We knew we had to help
When the pandemic hit, the demand for COVID-19 testing drastically increased, resulting in shortages of COVID-19 sampling and laboratory supplies, and impacting the number of tests that could be performed. When we confirmed that our collection devices could stabilize, and inactivate the SARS-CoV-2 virus, we knew we could help. Not only could OMNIgene®•ORAL and ORAcollect•RNA be used to combat test kit shortages, these devices could also make sample collection less painful for patients and protect healthcare professionals by enabling at-home self-collection. In addition, we were able to help with our prepIT·Q2A reagent which isn’t subject to the same reagent supply challenges as other extraction kits on the market.
If you want to learn more or have any questions for our speakers today, you can send us an email at firstname.lastname@example.org. If you wish to try samples of prepIT•Q2A, OMNIgene®•ORAL or ORAcollect•RNA kits, you can send us an email or click below to request free samples for evaluation.