3 results about "Virus Integration" patented technology

Among other things, provided herein are systems that replace the natural random integration activity of a retrovirus with site-specific integration machinery. This approach allows for a more precise targeting of a gene of interest into a human genome, e.g., for therapeutic purposes. The system may include integration-deficient retrovirus (e.g., lentivirus) (IDLV), in which the natural integration activity has been reduced (e.g., by mutation to the viral integrase polypeptide). Instead, the system may comprise a site-specific recombinase (e.g., a serine recombinase, e.g., a serine integrase) capable of directing insertion of a template DNA, or portion thereof, into a desired site in the human genome.

This invention discloses a detection method and application for simultaneously acquiring viral integrated transcripts and RNA modifications based on nanopore sequencing. The method includes: obtaining total RNA from a biological sample; separating and purifying the total RNA to obtain mRNA; ligating the mRNA to a reverse transcription adapter; ligating the reverse transcription adapter to a nanopore sequencing adapter; and using strand-specific sequencing, allowing a single-stranded library containing viral integrated mRNA to pass through a nanopore located on a chip without sequencing the complementary cDNA strand, simultaneously detecting viral integrated transcripts and RNA modification information. This method offers the advantages of long-fragment sequencing while simultaneously acquiring base modification information, achieving simple and accurate single-molecule level detection. Furthermore, this method avoids the biases inherent in reverse transcription and PCR, as well as the loss of RNA modification information during reverse transcription and amplification, preserving the natural properties of RNA and obtaining various base variations, structural variations, and modification information, thereby enabling the differentiation of highly similar isoforms and the identification of novel transcripts.

This invention provides a method for detecting integration sites and quantitatively assessing viral integration efficiency based on targeted capture sequencing. The method includes targeted enrichment and sequencing of samples using a targeted capture sequencing panel; performing virus-host dual-reference alignment and breakpoint clustering on the enriched sequencing data to achieve comprehensive detection of integration sites; and calculating the integration efficiency by comparing the abundance of virus-host fusion reads at each integration site with the total amount of virus-specific reads. This allows for simultaneous quantitative assessment of integration site profiles and integration efficiency in the same sequencing experiment. Compared to the LAM-PCR method, the TES Panel of this invention significantly improves the sensitivity and comprehensiveness of fragmented integration detection through multi-site, multi-fragment targeted capture, providing key technical support for quality control of gene therapy products, risk warning of viral infection-related diseases, and safety assessment.