The development of a SENsitive Splint-based one-step isothermal RNA detection (SENSR) method for rapid and straightforward onsite detection of pathogen RNAs with high sensitivity and specificity offers great potential for SARS-CoV-2 diagnosis. 


SENSR consists of two simple enzymatic reactions: a ligation reaction by SplintR ligase and subsequent transcription by T7 RNA polymerase. The resulting transcript forms an RNA aptamer that induces fluorescence. Compared to the conventional culture-based or immunoassay-based approaches, a nucleic acid-based approach relies primarily on a strand-displacing polymerase or T7 RNA polymerase at a constant temperature. In particular, the SplintR ligase can efficiently ligate two DNA probes using a target single-stranded RNA as a splint, enabling the sequence-specific detection of RNA molecules. 


SENSR integrates all component reaction steps using the specially designed probes that contain all required functional parts: promoter, hybridization sequence to target, and an aptamer template. Even with the multifaceted features of the SENSR probes, the design process is systematic and straightforward. The probe design is unique in that two DNA probes are designed to expose single-stranded target recognition parts, enabling hybridization of the target RNA and the probes at 37°C. 


SENsitive Splint-based one-step isothermal RNA detection (SENSR)

This method amplifies a DNA or RNA target sequence, but unlike PCR, does not need thermal cycling. These assays use isothermal methods to allow for primer binding and then amplify the selected strands using a polymerase with stand displacement activity. The amplified gene products are then detected via photometry. 

Isothermal Nucleic Acid Amplification

This method detects the total viral RNA from a cell culture supernatant and 19 nasopharyngeal swab samples. Uses isothermal methods for reverse transcription and then uses recombinase activity to promote primer binding to the respective dsDNA sequence. This process also achieves 100% specificity and sensitivity and offers advantages over the typical RT-PCR in efficiency and portability allowing for clinical decisions to be made real time when a patient visits. 

Uses recently discovered crRNA guided detection that is specific to viral RNA. The Cas13a enzyme that recognizes and binds targeted RNAs in a sequence-specific manner for signal amplification and nucleic acid detection.   

CRISPR

Unlike CRISPR, the Cas13a protein needs to be purified and is recombinantly expressed. Target site-recognition activates reporter probes resulting in fluorescence to recognize viral RNA. Assays can be designed as a paper dipstick test which delivers in 30-60 minutes. 


Cas13a Assay

NGS can sequence 30,000 nucleotides of the viral genome. This method provides insight on environmental monitoring, surveillance testing, and origin of the strain to pinpoint the viral evolution. 

Next Generation Sequencing

Diagnostic Testing methods that amplify DNA using reverse transcriptase.
Nucleic Acid Amplification Tests include but are not limited to:

- RT-PCR
- RT-LAMP
- Next Generation Sequencing
- Isothermal Nucleic Acid Amplification
- RPA

NAAT

Biosensors for COVID-19

Combining the excellent electrical and optical properties of nanomaterials with biological or synthetic molecules as receptors to detect selectively any kind of analyte, nanobiosensors are a valuable alternative to conventional diagnostic tools. 

- Graphene-based Field-Effect Transistor (FET) Biosensor

- Dual-Functional Plasmonic Biosensor

Paper/nanomaterial-based sensors, in general, and, particularly, NP-based lateral-flow devices that are observed with the naked eye or operated through a smartphone are now the most reported testing platforms for the analysis of COVID-19-related biomarkers. Nanopaper and nanochannels may also offer cost-efficient alternatives for detection of viruses and related biomarkers. 

Nanomaterials for COVID-19 Diagnosis

The Wondfo RCI functions by detecting IgM/IgG antibodies for SARS-CoV-2.  10 μL of plasma or serum are inserted into the testing device, and antibodies that fight against SARS-CoV-2 contained in the sample attach to recombinant antigens that cover colloidal gold particles, ultimately creating a complex of antigen-antibody/colloidal gold particles.  80 μL of buffer solution must also be inserted into the testing device under the sample cavity.  The results of the RCI can be read within 15 minutes.  A major limitation of RCI is that it is not capable of differentiating between acute disease and infection from the past.  


Wondfo Qualitative Rapid Chromatographic Immunoassay (RCI)

- Isothermal Nucleic Acid Amplification
- RPA
- CRISPR
- Cas13a Assay
- Next Generation Sequencing 
- Nanomaterials (nanotrap particles, etc.)
- Wondfo Qualitative Rapid Chromatographic Immunoassay (RCI)

University of California, Santa Cruz

Smith College

Johns Hopkins University

University of California, Davis

Key Features of Diagnostic Testing and Sampling

Specificity measures the ability for the test to produce a correct negative result for people who don't have a given condition.
ex) A test with a 80% sensitivity will return a correct positive result 85% of the time, but a a false negative 15% percent of the time.

Specificity in Testing

Biomedical engineers have put in extensive time and research in testing methods and diagnostics regarding the novel coronavirus. The test results of the population have provided mathematical models to visualize the pandemic, alternatively the private sector has produced a high-volume of nasopharyngeal, throat, and nasal test kits by bioengineering front-runners including: Abbot, Xpert, Lightmix, and Genmark.

Diagnostics and Testing with Biomedical Engineering

Sensitivity is a measure of how often a "true positive" result is produced. A test with a sensitivity of 85% will produce a "true positive" 85% and a false negative 15% of the time.

Sensitivity of Testing

Dcruz, R. J., Currier, A. W., & Sampson, V. B. (2020). Laboratory Testing Methods for Novel Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2). Frontiers in Cell and Developmental Biology, 8. doi:10.3389/fcell.2020.00468

Frontiers in Cell and Developmental Biology

Barclay, R., Akhrymuk, I., Patnaik, A., Callahan, V., Lehman, C., Andersen, P., . . . Lepene, B. (2020). Nanotrap® particles improve detection of SARS-CoV-2 for pooled sample methods, extraction-free saliva methods, and extraction-free transport medium methods. doi:10.1101/2020.06.25.172510

Nanotrap particles improve detection of SARS-CoV-2 for pooled sample methods, extraction-free saliva methods, and extraction-free transport medium methods

Currently Used Methods for Diagnosis

Emerging Methods for Diagnosis of SARS-CoV-2

Machine Learning models can be used to better understand the proteins and complexes that are incvolved with the novel Coronavirus. This includes producing predictions of pandemic regarding hospitalizations, patient outcomes, and simulations.

Machine Learning Analysis 

Sample Collection Methods for Diagnosis

- A reduction of ADAMTS13 levels can potentially predict mortality risk for patients infected with SARS-CoV-2

Potential Diagnostic Methods for COVID-19 Mortality Prediction  

Weekly surveillance testing along with isolation would more effectively limit COVID-19 outbreaks than the slow and expensive (yet precise) qPCR (quantitative polymerase chain reaction) testing method that is currently employed.

Testing Strategy for Controlling COVID-19 Outbreaks

In August, the CDC officially recommended that those without COVID-19 symptoms didn't need to be tested- even if they knew they'd been exposed. This decision received a lot of backlash from public health officials pushing for more testing.  It was later revealed that that the original guidelines had been re-written by those involved with the Department of Health and Human Services and the US COVID task force.

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