BK Virus Detection via Conserved Region Primers
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Solution Overview
Problem
Current diagnostic tests for BK virus lack sensitivity for detecting low titers and fail to differentiate between BK virus and other polyoma viruses like JC virus, leading to issues with false positives and false negatives, particularly in immunocompromised patients and renal transplant recipients.
Innovation Solution
The development of nucleic acid-based methods and kits that target conserved regions of the BK virus genome, using specific primer pairs and probes for real-time PCR, allowing for sensitive and specific detection of BK virus while avoiding detection of closely related viruses.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If existing diagnostic tests are used to detect polyomaviruses, then virus detection is possible, but sensitivity for detecting low titers is insufficient
Solution Approach 1:
The patent modifies detection parameters by targeting specific conserved genomic regions (control region and early region) with optimized primer pairs and probe sequences. This allows the assay to detect low viral titers effectively by changing the detection target from general polyomavirus sequences to specific BK virus regions with known conservation patterns across different strains.
Solution Approach 2:
The patent replaces conventional viral culture or indirect detection methods with direct nucleic acid detection using real-time PCR. This substitution enables sensitive detection of viral DNA even at low titers, eliminating the need for viral isolation and reducing false negatives associated with culture-based methods.
2Measurement precision
If existing diagnostic tests are used to detect polyomaviruses, then virus detection is possible, but specificity to differentiate BK virus from other polyoma viruses is insufficient
Solution Approach 1:
The patent applies local quality by designing primers and probes that target specific conserved regions unique to BK virus (control region and early region) rather than using general polyomavirus sequences. This localized targeting ensures the assay specifically detects BK virus while avoiding cross-reaction with JC virus or other polyomaviruses, thereby reducing false positives.
Solution Approach 2:
The patent segments the detection strategy by using multiple specific primer pairs targeting different conserved regions (control region and early region) of BK virus. This segmentation allows the assay to maintain high specificity through region-specific priming while ensuring comprehensive detection across different viral strains and genotypes.
3Measurement precision
If detection assays target variable regions of BK virus genome, then detection of specific strains is possible, but detection of different BK virus genotypes becomes unreliable
Solution Approach 1:
The patent changes the detection approach by targeting conserved regions (control region and early region) that maintain sequence conservation across different BK virus genotypes and strains. This parameter change from variable to conserved regions ensures the assay reliably detects all BK virus genotypes while still providing strain-specific information through sequence analysis of the amplified products.
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
These methods provide rapid, reliable, and specific detection of BK virus, reducing false positives and negatives, and are suitable for both diagnostic and therapeutic monitoring in clinical settings.
Implementation Method 1
The invention provides methods and compositions for rapid, sensitive, and highly specific nucleic acid-based (e.g., DNA based) detection of a BK virus in a sample. The methods involve detecting a target nucleic acid having a target sequence of conserved regions of BK viral genome.
Implementation Method 2
The invention features primer pairs and kits, for use in the methods of the invention.
Data Source
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AI summary
The invention provides methods and compositions for rapid, sensitive, and highly specific nucleic acid-based (e.g., DNA based) detection of a BK virus in a sample. In general, the methods involve detecting a target nucleic acid having a target sequence of a conserved region of BK viral genomes. The invention also features compositions, including primers, probes, and kits, for use in the methods of the invention.