Extraction Composition for Direct Pathogen Detection

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Solution Overview

Problem

Current methods for detecting pathogens like SARS-CoV-2 require time-consuming nucleic acid purification steps, leading to delays and reduced sensitivity, especially during pandemics, and existing direct detection methods in transport media suffer from inhibition and reduced sensitivity.

Innovation Solution

A method using an extraction composition containing surfactants, nuclease inhibitors, and reducing agents to prepare biological samples for direct amplification without prior purification, allowing for increased sensitivity and reduced processing time by enabling the use of larger sample volumes in amplification reactions.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If nucleic acid purification is performed before amplification, then amplification sensitivity is maintained, but processing time increases and productivity decreases

Engineering Contradiction:

Improveamplification sensitivityVSAvoidprocessing speed

Core Design Contradiction:

Measurement precisionVSProductivity

Solution Approach 1:

The invention combines the sample preparation step with the amplification step into a single unified process. The extraction composition is mixed directly with the biological sample and then subjected to amplification without intermediate purification steps, merging two previously separate operations into one continuous process that maintains sensitivity while improving throughput

Inventive Principle:

Principle #5Merging (Combining)

Solution Approach 2:

The invention extracts and removes inhibition components from the reaction system by using a specially designed extraction composition that contains inhibitors of nucleases and other interfering substances. This selective extraction allows the target nucleic acid to be amplified while harmful components are neutralized or removed

Inventive Principle:

Principle #2Taking out (Extraction)

2Productivity

If direct amplification without purification is performed, then processing time decreases and productivity increases, but amplification sensitivity decreases due to inhibition

Engineering Contradiction:

Improveprocessing speedVSAvoidamplification sensitivity

Core Design Contradiction:

ProductivityVSMeasurement precision

Solution Approach 1:

The invention introduces an extraction composition as an intermediary substance between the biological sample and the amplification reaction. This intermediary contains nuclease inhibitors and other protective agents that mediate the interaction, allowing direct amplification while protecting the target nucleic acid from degradation and inhibition

Inventive Principle:

Principle #24Intermediary (Mediator)

Solution Approach 2:

The invention changes the chemical parameters of the reaction environment by using a specially formulated extraction composition with optimized pH, ionic strength, and inhibitor concentrations. These parameter changes create conditions that allow direct amplification to proceed with high sensitivity despite the presence of complex biological samples

Inventive Principle:

Principle #35Parameter changes

3Measurement precision

If larger sample volumes are used in amplification, then detection sensitivity increases, but inhibition from sample components increases

Engineering Contradiction:

Improvedetection sensitivityVSAvoidinhibition from sample components

Core Design Contradiction:

Measurement precisionVSObject-affected harmful factors

Solution Approach 1:

The invention converts the harmful effect of sample components into a beneficial outcome by using the extraction composition to selectively inhibit nucleases and other degrading enzymes present in the sample. The same components that could cause inhibition are transformed into a protective environment that preserves target nucleic acid integrity

Inventive Principle:

Principle #22Blessing in disguise (Convert harm into benefit)

Solution Approach 2:

The invention uses a composite extraction composition containing multiple functional components including nuclease inhibitors, buffer agents, and protective compounds. This composite material provides multifunctional protection against various inhibition mechanisms while allowing the target nucleic acid to remain accessible for amplification

Inventive Principle:

Principle #40Composite materials

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 enhances the sensitivity and speed of pathogen detection by eliminating the need for nucleic acid purification and reducing pre-processing steps, making it suitable for rapid processing of multiple samples, particularly during pandemics.

Implementation Method 1

An extraction composition is used which comprises (a) at least one surfactant, (b) at least one nuclease inhibitor, and (c) optionally at least one reducing agent

Methodology Applied

Scientific EffectSurfactant: Surfactant

Implementation Method 2

at least one nuclease inhibitor

Methodology Applied

Scientific EffectNuclease inhibition: Enzyme

Data Source

PatentUS20230357823A1Pathogen detection method

Publication Date: 2023.11.09 QIAGEN GMBH

AI summary

The present invention provides method and kits for amplification based detection of target nucleic acids and pathogens using crude biological samples without prior target purification.