Programmable low-cost DNA-based platform for viral RNA detection

virus199

https://advances.sciencemag.org/content/early/2020/08/20/sciadv.abc6246

Abstract

Detection of viruses is critical for controlling disease spread. Recent emerging viral threats including Zika virus, Ebola virus, and SARS-Cov-2 (responsible for COVID-19) highlight the cost and difficulty in responding rapidly. To address these challenges, we develop a platform for low-cost and rapid detection of viral RNA with DNA nanoswitches that mechanically reconfigure in response to specific viruses. Using Zika virus as a model system, we show non-enzymatic detection of viral RNA, with selective and multiplexed detection between related viruses and viral strains. For clinical-level sensitivity in biological fluids, we paired the assay with sample preparation using either RNA extraction or isothermal pre-amplification. Our assay requires minimal lab infrastructure, and is adaptable to other viruses, as demonstrated by quickly developing DNA nanoswitches to detect SARS-CoV-2 RNA in saliva. We expect further development and field implementation will improve our ability to detect emergent viral threats and ultimately limit their impact.

virus199

Efficient high-throughput SARS-CoV-2 testing to detect asymptomatic carriers

https://advances.sciencemag.org/ ... 8/20/sciadv.abc5961

Abstract
Recent reports suggest that 10-30% of SARS-CoV-2 infected patients are asymptomatic and that significant viral shedding may occur prior to symptom onset. Therefore, there is an urgent need to increase diagnostic testing capabilities to prevent disease spread. We developed P-BEST - a method for Pooling-Based Efficient SARS-CoV-2 Testing which identifies all positive subjects within a large set of samples using a single round of testing. Each sample is assigned into multiple pools using a combinatorial pooling strategy based on compressed sensing designed for maximizing carrier detection. In our current study we pooled sets of 384 samples into 48 pools providing both an 8-fold increase in testing efficiency, as well as an 8-fold reduction in test costs. We successfully identified up to 5 positive carriers within sets of 384 samples. We then used P-BEST to screen 1115 healthcare workers using 144 tests. P-BEST provides an efficient and easy-to-implement solution for increasing testing capacity that can be easily integrated into diagnostic laboratories.