SARS-CoV-2 Detection Oligonucleotides for Rapid Assay
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Solution Overview
Problem
The global outbreak of COVID-19 caused by SARS-CoV-2 has highlighted the need for rapid and reliable molecular assays to diagnose infected individuals, as the virus can spread from asymptomatic carriers, leading to public health and economic stresses, and current methods are inadequate for early and sensitive detection.
Innovation Solution
Development of oligonucleotides and kits that target specific nucleic acid sequences from the SARS-CoV-2 virus, particularly the N protein and S protein genes, for use in PCR assays to detect the presence of SARS-CoV-2 in biological samples, differentiating it from other coronaviruses and providing sensitive and specific results.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If conventional detection methods are used for SARS-CoV-2, then the detection process is simple to perform, but the sensitivity and reliability of detection are insufficient
Solution Approach 1:
The detection assay is divided into multiple independent components including specific oligonucleotide primers and probes targeting different regions of SARS-CoV-2 genome (N gene, S gene, E gene), allowing modular assembly and systematic detection that improves reliability while maintaining manageable complexity
Solution Approach 2:
The assay system is designed with universal components that can detect multiple SARS-CoV-2 genomic regions simultaneously, and the methodology can be adapted to detect other coronaviruses, providing multi-functional capability that enhances detection reliability across different viral targets
2Productivity
If rapid detection is implemented to identify infected individuals early, then the spread of virus can be reduced, but the detection method must be both sensitive and specific which increases complexity
Solution Approach 1:
Specific oligonucleotide primers and probes are pre-designed and prepared to target conserved regions of SARS-CoV-2 genome, enabling rapid amplification and detection without requiring complex sample preparation or multiple testing steps, thus achieving fast detection with controlled complexity
Solution Approach 2:
The assay utilizes optimized thermal cycling parameters and fluorescent detection thresholds to achieve rapid results, where controlled changes in temperature profiles and detection sensitivity parameters enable fast turnaround while maintaining assay specificity and managing overall system complexity
3Measurement precision
If specific oligonucleotides targeting N protein and S protein genes are used, then detection precision and ability to differentiate from other coronaviruses is improved, but the complexity of assay design and implementation increases
Solution Approach 1:
The assay employs locally optimized oligonucleotide sequences that specifically target unique regions within the N gene, S gene, and E gene of SARS-CoV-2, providing high detection precision for specific viral components while keeping the overall assay design manageable through focused targeting
Solution Approach 2:
Fluorescently labeled probes serve as intermediaries that specifically bind to target sequences in the N, S, and E genes, translating genetic information into detectable signals with high precision while simplifying the detection mechanism and reducing overall assay design complexity
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
The described methods and kits enable rapid and accurate detection of SARS-CoV-2, reducing the spread of the virus by identifying infected individuals early, thereby aiding in public health responses and treatment decisions.
Implementation Method 1
The disclosed oligonucleotides, methods, and kits can be used in an assay to detect the presence or absence of SARS-CoV-2 virus in a biological sample
Implementation Method 2
The disclosed assays target specific nucleic acid sequences from the genome of the SARS-CoV-2 virus, in particular, regions in the nucleocapsid protein (N protein) gene and spike protein (S protein) gene of SARS-CoV-2
Data Source
AI summary
Methods, kits, and oligonucleotides used in the detection of the coronavirus strain, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are disclosed. In some aspects, the oligonucleotides are primers or probes used in the described methods or kits. The oligonucleotide consists of 42 or less nucleotides and has a nucleotide sequence that consists essentially of, or is a variant of, the nucleotide sequence of: SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:6, or SEQ ID NO:7. In some embodiments, the oligonucleotide is modified with an internal spacer or a detectable label. For example, the 5′ terminus is labeled with a fluorophore and the 3′ terminus is complexed to a quencher of fluorescence of said fluorophore. In some embodiments, the nucleotide sequence of the oligonucleotide further comprises a universal tail sequence.