Strain-Independent Pathogen Amplification via Multiple Primer Pairs
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Solution Overview
Problem
Current vaccines against rapidly mutating pathogens like HIV are ineffective due to their reliance on consensus sequences, which fail to target multiple variants and can increase pathogen load, and existing amplification methods struggle to account for high mutation rates and sequence variability.
Innovation Solution
Development of methods for strain-independent nucleic acid amplification of pathogens using multiple primer pairs that compensate for sequence variability, allowing for the production of nucleic acids encoding multiple variants, which can be used to create patient-specific vaccines by loading antigen-presenting cells or administering directly as nucleic acid vaccines.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of manufacture
If consensus sequences are used as immunogens in vaccines, then vaccine production is simplified, but the vaccine fails to target multiple HIV variants and can increase pathogen load
Solution Approach 1:
The patent segments the HIV genome into multiple distinct variant sequences rather than using a single consensus sequence. Multiple nucleic acid sequences representing different HIV variants are individually synthesized and combined to create a vaccine composition that targets diverse viral strains simultaneously
Solution Approach 2:
The patent changes the fundamental parameter of vaccine composition from a single consensus sequence to multiple variant-specific sequences. By altering the sequence diversity parameter and incorporating multiple distinct HIV variant sequences, the vaccine achieves broader coverage while maintaining manufacturability through synthetic biology approaches
2Adaptability or versatility
If total pathogen RNA is used to load antigen presenting cells, then comprehensive antigen coverage is achieved, but pathogen load in the patient increases
Solution Approach 1:
The patent extracts only the essential antigenic components from the total pathogen RNA. Instead of using complete viral genomes that could replicate and increase pathogen load, the invention isolates and synthesizes specific nucleic acid sequences encoding antigenic regions, delivering only the immunogenic portions without the harmful replicative capacity
Solution Approach 2:
The patent uses synthetic nucleic acid sequences that are non-replicating and transient rather than complete pathogen genomes. These synthetic sequences serve their immunogenic purpose and are naturally degraded without persisting or replicating in the patient, avoiding the creation of a self-sustaining pathogen load
3Device complexity
If standard PCR amplification is used on highly mutated HIV genomes, then amplification process is simple, but amplification efficiency decreases due to high mutation rates and sequence variability
Solution Approach 1:
The patent applies local quality by designing primers with variable regions that specifically match different HIV variant sequences. Rather than using uniform primers that may not bind efficiently to highly mutated regions, the invention creates primer sets with locally adapted sequences that match specific variant regions, ensuring efficient amplification across diverse strains
Solution Approach 2:
The patent creates a universal amplification system that can handle multiple HIV variants simultaneously. By designing degenerate primers or primer pools that can bind to multiple variant sequences, the system achieves broad amplification capability across different HIV strains while maintaining a relatively simple overall process
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 enables the creation of vaccines that effectively target multiple HIV variants, reducing the risk of pathogen load increase and improving immune response specificity, while avoiding the need for full pathogen genome amplification, thus minimizing adverse effects.
Implementation Method 1
amplification of pathogen nucleic acid from an infected subject using multiple primer pairs that compensate for sequence variability
Implementation Method 2
nucleic acid amplification of pathogen nucleic acid
Data Source
AI summary
This in invention relates to methods for the nucleic acid amplification of multiple variants (strains) of any pathogen present in a sample, and preferably in a sample from a pathogen infected individual. In preferred embodiments, the pathogen is a retrovirus, such as HIV. The amplified pathogen nucleic acid can be used to identify the pathogen variants present in a sample, to quantitate the pathogen present in a sample, and as a nucleic acid vaccine, or in the preparation of antigen presenting cell vaccines. Nucleic acids produced by the methods of the invention or the proteins encoded thereby can be used to transfect/load antigen presenting cells. The loaded antigen presenting cells can then be used as a vaccine for the treatment of pathogen infection. In another embodiment, nucleic acids produced by the methods of the invention can be used directly as nucleic acid vaccines without prior loading into antigen presenting cells.