Multiplex Viral Nucleic Acid Detection with Specific Oligomer Probes
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Solution Overview
Problem
Current methods for detecting adenovirus, metapneumovirus, and rhinovirus are limited by their inability to rapidly, sensitively, and specifically identify multiple serotypes and subtypes, often requiring time-consuming and expensive processes that may lead to false positives.
Innovation Solution
The use of specific amplification oligomers targeting defined nucleotide positions within the adenovirus, metapneumovirus, and rhinovirus genomes, combined with detection probes, to amplify and detect these viruses with high sensitivity and specificity.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of operation
If conventional serological tests and cell culture methods are used for adenovirus detection, then the detection process is simple to perform, but the detection speed is slow and sensitivity is reduced
Solution Approach 1:
The patent replaces conventional mechanical/cellular methods (cell culture) and traditional biochemical methods (serological tests) with a molecular biology-based PCR system. This substitution enables rapid amplification of viral DNA sequences, achieving detection within hours rather than days or weeks, while maintaining operational simplicity through standardized reagent kits.
Solution Approach 2:
The patent employs preliminary action by pre-designing and pre-synthesizing specific oligonucleotide primers and probes that target conserved regions of adenovirus genomes across multiple species. These pre-prepared reagents are included in detection kits, allowing immediate PCR amplification without requiring preliminary virus cultivation or complex sample preparation steps.
2Measurement precision
If PCR-based assays with low stringency conditions are used to detect genetically diverse adenoviruses, then the detection sensitivity increases, but the measurement precision decreases leading to false positives
Solution Approach 1:
The patent applies local quality by designing detection systems with different stringency levels for different stages: initial amplification uses moderate stringency to capture diverse adenovirus sequences, while subsequent detection steps using specific probes targeting unique regions of amplified products apply high stringency to ensure species-specific identification. This localized application of quality control at different process stages resolves the contradiction between sensitivity and specificity.
Solution Approach 2:
The patent segments the detection process into multiple distinct steps: (1) initial PCR amplification using primers targeting conserved regions to ensure broad detection, (2) secondary amplification or nested PCR using species-specific primers for confirmation, and (3) probe-based detection for final identification. This segmentation allows each step to optimize for its specific function, maintaining both sensitivity and reliability.
3Measurement precision
If multiple separate assays are used to detect different adenovirus species, then the measurement precision for each species is high, but the device complexity and time required increase
Solution Approach 1:
The patent implements universality by developing a hierarchical detection system where a single set of outer primers can amplify all adenovirus species, and within that framework, species-specific inner primers and probes provide targeted identification. This multi-functional system allows one PCR reaction mixture to potentially detect multiple species simultaneously, reducing the need for separate assays while maintaining species-specific precision through the nested design.
Solution Approach 2:
The patent employs the nested doll principle by designing nested PCR assays where outer primers define a broad amplification region encompassing all adenovirus species, and inner species-specific primers nest within this region to amplify smaller, species-specific segments. This nested structure allows sequential detection from general to specific, reducing complexity by combining multiple detection capabilities in a hierarchical framework rather than requiring parallel separate assays.
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
Enables rapid, sensitive, and specific detection of multiple adenovirus serotypes, metapneumovirus subtypes, and rhinovirus strains, reducing the need for skilled technicians and minimizing false positives.
Implementation Method 1
the first amplification oligomer and second amplification oligomer are configured to amplify an Adenovirus amplicon
Implementation Method 2
hybridization between the detection probe oligomers and the target nucleic acid to which the detection probe oligomer is configured to hybridize indicates the presence of that target nucleic acid
Data Source
AI summary
The disclosed disclosure is related to methods, compositions, and kits for targeting Adenovirus, Metapneumovirus, and/or Rhinovinis nucleic acid. Compositions include amplification oligomers and/or detection probe oligomers. Kits and methods comprise at least one of these oligomers. Methods include uniplex and multiplex amplification and detection reactions.