Advanced Microarray Testing Guides Public Health Decision Making
Improved testing platforms with greater specificity, throughput, and environmental testing capabilities are essential to support public health decisions
PathogenDx developed DetectX-RV technology that combines routine RT-PCR technology with DNA microarray to improve COVID-19 diagnostic sensitivity, especially for pre-symptomatic individuals.
Scientists, public health officials, and political leaders face the same recurring question: how and when can the public return to a normal way of life in the wake of the COVID-19 pandemic? Scientists, public health officials, and political leaders face the same recurring question: how and when can the public return to a normal way of life in the wake of the COVID-19 pandemic? While it is currently unclear when social distancing regulations will be reduced, and when schools and workplaces will reopen, widespread testing will be critical to ensure these measures are not lifted prematurely. However, the current COVID-19 diagnostic technology is now thought to display a relatively high false negative rate and thus may lack the sensitivity to support population studies of pre-symptomatic individuals or for environmental testing, such as the air or surfaces in public spaces.
PathogenDx developed DetectX-RV technology that combines routine RT-PCR technology with DNA microarray to improve COVID-19 diagnostic sensitivity, especially for pre-symptomatic individuals, and the EnviroX-RV platform supports environmental analysis of COVID-19. Together, these platforms may be used to guide the transition into a new normal.
Current COVID-19 diagnostic methods are based on real-time polymerase chain reaction (RT-PCR) methods, which detect viral RNA in samples obtained by nasopharyngeal swabs. RT-PCR detects one or a few viral RNA target sequences via RNA isolation, reverse transcription, amplification, and analysis. Despite its widespread use, RT-PCR is limited in its low end sensitivity, and may thus fail to detect viral infection in weakly symptomatic or pre-symptomatic individuals. This contributes to one of the largest challenges in tracking and containing the spread of COVID-19: identifying asymptomatic or mildly symptomatic carriers. These individuals are often unaware they are infected, but can potentially infect numerous others. As these patient samples often contain only a small amount of viral RNA, current diagnostic testing methods may lack the sensitivity to detect such individuals relative to the backdrop of a relatively high false negative rate. The issue is that RT-PCR hits the “ragged edge” in terms of detecting low viral loads where the ”signal to background” ratio converges, thus resulting in the false negatives.
DetectX-RV combines routine RT-PCR technology with DNA microarray for significantly greater low end sensitivity and can thus reduce the risk of false negatives, particularly among asymptomatic and mildly symptomatic individuals. Following RNA extraction, and amplification, the cDNA is labeled with a fluorophore and added to the DNA microarray containing 144 synthetic ssDNA probes arranged in a 12 x 12 configuration. This technique enables detection of multiple viral RNA target sequences simultaneously in the same sample and can thus detect viral RNA present at lower copy number, via confirmatory multiple-site detection of the same viral genome. As such, DetectX-RV can achieve a higher degree of sensitivity among asymptomatic individuals to support more accurate diagnosis and contact tracing efforts. In this particular case, the DetectX-RV generates a signal-to-background intensity of 30-40x giving the range to detect low-viral loads without getting “drowned out” by background.
In addition to accuracy, higher throughput is essential to support widespread testing. The DetectX-RV microarray enables simultaneous testing of 12 individual samples per slide, processing up to 16 slides (192 specimens) within 6-8 hours. With automation, the system delivers 576 specimens in one 8 hour shift. With a log difference in its signal-to-background to RT-PCR, this platform may potentially be used for pooled samples, which would dramatically improve efficiency and provide insights into the effectiveness of social distancing measures. For example, it would take the same amount of time to test a single individual using current methods as it would to pool 10 samples and test them simultaneously using an advanced platform. A negative test result for the pooled samples would rule-out infection in a larger group, accelerating testing, and providing better insights into the infection rate within the population. Not to mention, saving significant reagent and lab supplies given what we are facing now and for the next 12 months.
The SARS-CoV-2 virus can persist on various surfaces from hours to days. Environmental testing is therefore essential to identify which shared or public spaces may require decontamination and to assess whether it is safe for individuals to return to a workspace or school. PathogenDx also developed the EnviroX-RV platform that combines the power of the DetectX-RV platform with a bioaerosol and surface swab collection technology. It features collection capability in a liquid output that can be rapidly analyzed within 8 hours, with a high degree of sensitivity and specificity compared to many RT-PCR methods.
When social distancing measures will begin to lift, and it will be deemed safe to return to work and school remains uncertain. It is clear, however, that robust, accurate testing will be necessary to support decisions surrounding public health