Multiplex SARS-CoV-2 Variant Detection With Dual-Function Fluorophores
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Solution Overview
Problem
Existing multiplex PCR systems are limited by the number of fluorophores they can accommodate, restricting the identification of multiple nucleic acid sequences to four or fewer, and methods for detecting viral, bacterial, and fungal variants are costly and inefficient.
Innovation Solution
A method using a combination of specific and semi-specific fluorophore signals to detect genomic variants, allowing detection of multiple variants with fewer fluorophores and channels, such as using two fluorophores for three genomic variants in a two-channel PCR machine.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If multiple fluorophores are used to detect multiple nucleic acid sequences in multiplex PCR, then the identification capability increases, but the cost increases and the machine capability requirements increase
Solution Approach 1:
A single fluorophore signal serves multiple functions by detecting both a specific target sequence and a semi-specific target sequence. The first signal detects a first target sequence specific to a first variant, and also detects a second target sequence that is semi-specific and common to multiple variants, thereby reducing the total number of fluorophores needed while maintaining identification capability.
Solution Approach 2:
The patent combines the detection of specific and semi-specific target sequences into a single fluorophore channel. By merging these detection functions into one signal, the system reduces the number of separate fluorophores and machine channels required, while still enabling differentiation between multiple viral variants through pattern recognition of the detected sequences.
2Measurement precision
If a one-to-one ratio of fluorophore per target nucleic acid sequence is used, then each target can be uniquely identified, but the number of target sequences that can be detected is limited to 3 with a four-channel machine
Solution Approach 1:
One fluorophore signal performs multiple detection functions simultaneously - it identifies a specific target sequence unique to one variant and also detects a semi-specific target sequence shared by multiple variants. This multi-functionality allows the system to detect more target sequences than the number of fluorophores used, breaking the one-to-one limitation.
Solution Approach 2:
The patent adds a dimensional layer of interpretation by analyzing patterns of detection across multiple target sequences detected by fewer fluorophores. Instead of mapping one fluorophore to one target, the system uses combinatorial patterns of detection results to uniquely identify multiple variants, effectively adding an informational dimension that increases productivity without requiring additional physical channels.
3Adaptability or versatility
If multiple fluorophores are used to detect multiple variants, then variant detection capability improves, but the cost and complexity of the assay increases
Solution Approach 1:
The assay reduces complexity by making one fluorophore signal universal for detecting both specific and semi-specific target sequences. This design simplifies the assay protocol, reagent preparation, and data interpretation compared to using separate fluorophores for each target, while maintaining the capability to detect and differentiate multiple viral variants through pattern recognition.
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
This approach efficiently detects multiple genomic variants with reduced resource use, enabling cost-effective identification of viral, bacterial, and fungal variants, including SARS-CoV-2 variants like Omicron and Delta, and informs targeted treatment strategies.
Implementation Method 1
The amplified nucleic acid sequences or amplicons are identified using multiple signals, such as for example, fluorophores
Data Source
AI summary
Methods are provided for detecting the presence of a specific genomic variant in a multiplex assay and distinguishing it from other genomic variants by interrogating one or more genomic loci specific to a particular genomic variant, and one or more semi-specific genomic loci present in in at least two genomic variants. The methods are useful for detecting a SARS-CoV-2 variant in a sample.