Pathogen Nucleic Acid Detection With Heat Inactivation and PCR
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Solution Overview
Problem
There is a need for effective methods and systems to detect SARS-CoV-2 and its variants due to the severity of the disease it causes and the emergence of new variants, necessitating rapid and accurate detection techniques.
Innovation Solution
The method involves obtaining a sample, inactivating any pathogens present, optionally concentrating the pathogen, isolating pathogen-specific nucleic acid, and detecting its presence through techniques like PCR amplification using specific primers and probes, with systems that include robotic stations and computer-program products for automation.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If manual pathogen detection methods are used, then detection accuracy can be maintained, but processing time is excessive and safety risks increase due to handling live pathogens
Solution Approach 1:
The system performs preliminary inactivation of pathogens in the sample before nucleic acid extraction and detection. By inactivating the pathogen first (through heat, chemicals, or other methods), the system eliminates safety risks and reduces subsequent processing time while maintaining detection accuracy, as the nucleic acid remains intact for PCR amplification
Solution Approach 2:
The system replaces manual mechanical handling of live pathogens with automated inactivation processes and robotic nucleic acid extraction. This substitution eliminates the need for personnel to handle live pathogens, improving safety while reducing processing time through automation
2Productivity
If manual processing of samples is used, then flexibility in handling different samples is maintained, but throughput is limited and safety exposure increases
Solution Approach 1:
The system automatically inactivates pathogens in all samples before processing, eliminating safety exposure risks. This preliminary action allows high-throughput processing of multiple samples simultaneously without increasing safety risks, as the inactivation step is performed on all samples before any manual or automated handling
Solution Approach 2:
The system uses automated robotic systems for nucleic acid extraction and PCR setup, replacing manual handling. This automation increases throughput by processing multiple samples in parallel while eliminating human exposure to pathogens through the prior inactivation step
3Measurement precision
If comprehensive pathogen detection protocols are used, then detection accuracy is improved, but processing time and complexity increase
Solution Approach 1:
The system combines multiple detection targets (SARS-CoV-2 and variant-specific nucleic acid sequences) into a single integrated PCR assay. By using multiple primers and probes in one reaction, the system achieves comprehensive detection accuracy without requiring separate processing steps for each target, thus reducing overall process complexity
Solution Approach 2:
The system uses a universal inactivation protocol that works for all pathogen types and a flexible PCR assay that can detect multiple targets simultaneously. This multi-functionality allows the same basic workflow to handle different samples and detection requirements, reducing the need for multiple specialized protocols and equipment
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 method enables rapid detection of SARS-CoV-2 and variants within a day, improving throughput and safety by automating processes, and using specific primers and probes for accurate results.
Implementation Method 1
the sample may be heated to inactivate the pathogen
Implementation Method 2
a protease may be added to the sample to inactivate the pathogen
Implementation Method 3
treating the heat-inactivated and optionally concentrated sample to isolate a pathogen-specific nucleic acid from the sample
Implementation Method 4
amplifying at least one target sequence of the SARS-CoV-2 cDNA
Data Source
AI summary
Disclosed are methods, compositions and systems for detecting the presence or absence of a pathogen in a sample. The method may include the steps of obtaining a sample from the subject and treating the sample with heat to inactivate any pathogen present in the sample. The method may further include the step of treating the sample to concentrate any pathogen present in the sample. Also, the method may include isolate a pathogen-specific nucleic acid from the heat-inactivated sample and detecting the presence or absence of the isolated pathogen-specific nucleic acid. In certain embodiments, the methods and/or systems may be used to detect SARS-CoV-2. The method may employ real time RT-PCR to provide results in about 3 hours or less.