Deep RNA Sequencing for Rapid Pathogen Identification
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Solution Overview
Problem
Current methods for diagnosing and treating COVID-19 and sepsis are hindered by the time-consuming process of RNA sequencing, which requires conversion to DNA, and the limited availability of direct diagnostic tests for identifying antibodies and bacterial pathogens.
Innovation Solution
Development of a method and computational tool to identify antibodies produced by COVID-19 patients using deep RNA sequencing, along with the creation of molecular diagnostic tests, including PCR tests, that can directly detect bacterial RNA from blood without the need for culture, enabling rapid identification of pathogens and resistance genes.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If RNA sequencing is performed using conventional DNA conversion methods, then diagnostic accuracy is improved, but time consumption increases
Solution Approach 1:
The patent extracts and analyzes only the unmapped portion of RNA sequencing data that corresponds to bacterial pathogens, rather than converting all RNA to DNA for comprehensive analysis. This selective approach removes unnecessary steps while maintaining diagnostic accuracy for sepsis and COVID-19 detection.
Solution Approach 2:
The patent performs preliminary RNA sequencing and identification of unmapped reads before final diagnostic interpretation. By pre-identifying bacterial RNA sequences in the unmapped portion, the system prepares diagnostic information in advance, reducing the time needed for final pathogen identification and treatment decisions.
2Measurement precision
If de novo antibody discovery and testing is performed, then antibody identification accuracy is improved, but development time increases
Solution Approach 1:
The patent performs preliminary analysis of RNA sequencing data to identify antibody-related sequences and bacterial pathogens before initiating full antibody discovery and testing protocols. This advance identification narrows the scope of subsequent testing, maintaining accuracy while reducing overall development time for therapeutic antibodies.
3Measurement precision
If comprehensive RNA sequencing analysis is performed, then pathogen detection accuracy is improved, but processing complexity increases
Solution Approach 1:
The patent extracts and focuses analysis specifically on the unmapped portion of RNA sequencing data, which contains bacterial pathogen sequences. By isolating this specific subset of data rather than analyzing the entire sequencing dataset, the system maintains high pathogen detection accuracy while significantly reducing computational and processing complexity.
Solution Approach 2:
The patent segments the RNA sequencing analysis into distinct components: mapped reads for host analysis and unmapped reads for pathogen detection. This segmentation allows separate, optimized processing pipelines for each component, reducing overall system complexity while maintaining comprehensive diagnostic accuracy.
4Reliability
If traditional culture methods are used for pathogen identification, then treatment accuracy is improved, but time to diagnosis increases
Solution Approach 1:
The patent replaces traditional mechanical culture methods with molecular RNA sequencing analysis. By detecting bacterial RNA directly in the unmapped portion of sequencing data, the system eliminates the time-consuming culture growth phase while maintaining reliable pathogen identification and treatment guidance through molecular characterization.
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 allows for the rapid identification of critical intervention points in COVID-19 patients and provides a faster diagnostic process for sepsis, enabling timely antibiotic treatment and improving patient outcomes.
Implementation Method 1
reverse transcription and amplification of bacterial RNA
Implementation Method 2
amplification of bacterial RNA
Data Source
AI summary
The invention provides a method for treating COVID-19 patients. Therapeutic antibodies of certain types of antibodies to COVID-19 are identified early by targeted diagnostic testing can be given to other COVID-19 patients to enhance their recovery. This invention also identifies bacterial pathogens, particularly those that are resistant to antibiotics, faster. Data from deep RNA sequencing of human blood is used to create a faster diagnostic test for infections and associated antimicrobial resistance. This invention thus also allows for appropriate antibiotic treatment at an earlier time point. The invention further provides improvements to RNA sequencing that can make RNA sequencing useful for diagnostic and therapeutic methods of treating sepsis. RNA sequencing can identify bacterial pathogens directly from the blood of patients with those infections.