10 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.

The invention provides an antiviral drug screening method and system based on inductive hypergraph learning, and a medium, and belongs to the technical field of bioinformatics, computational biology and artificial intelligence crossing, and the method comprises the following steps: S1, constructing a virus-drug adjacency matrix; s2, calculating a virus integration similar matrix and a drug integration similar matrix; s3, extracting statistic eigenvectors and graph theory eigenvectors of the viruses and the drugs and potential eigenvectors of the virus-drug pairs, and respectively merging the statistic eigenvectors and the graph theory eigenvectors according to rows to obtain a virus total eigenmatrix and a drug total eigenmatrix; s4, solving the target function by adopting a dual coordinate descent method to obtain an optimized projection parameter matrix; s5, calculating prediction scores from a virus perspective and a drug perspective, and averaging results to obtain a final virus-drug association prediction score matrix; and S6, screening the score of the row where the target virus is located, and sorting to obtain a final prediction result. The method not only improves the prediction performance, but also has good adaptability and popularization capability.

The invention provides an expression cassette for reducing lentivirus integration risk and application and a product thereof, and belongs to the technical field of gene engineering. According to the invention, further optimization is carried out based on the prior art, reverse assembly is carried out on an expression cassette, and optimization selection of a polyA sequence finds that the vector disclosed by the invention can improve the gene expression quantity of a single copy and realize the same expression effect with a relatively low lentivirus integration copy number, so that the risk caused by virus integration is further reduced.

The invention provides an antiviral drug screening method and system based on high-dimensional features and a storage medium, and belongs to the technical field of bioinformatics, computational biology and artificial intelligence crossing. Calculating a drug integration similar matrix and a virus integration similar matrix; based on an automatic encoder and a graph convolutional network, combining an adjacent matrix, a virus integration similar matrix and a drug integration similar matrix to construct a high-dimensional feature set; constructing a hypergraph by taking the high-dimensional feature set as a vertex set, defining a target function based on the hypergraph, and solving to obtain a projection matrix; calculating a prediction score matrix based on the projection matrix and the high-dimensional feature set; and based on the prediction score matrix, screening out the score of the row where the target virus is located, and sorting to obtain a final prediction result. According to the invention, through fusion of multiple similarities, the internal relationship of virus drugs is described more comprehensively, and the prediction performance is improved; the automatic encoder can learn a potential nonlinear relationship between samples, and the generalization ability of the model is enhanced.

Disclosed are compositions and methods for studying a Tat gene. Specifically, the disclosure provides a vector comprising a double-stranded nucleic acid construct which comprises a Tat gene and a green fluorescent protein (GFP) reporter element, and further wherein the double-stranded nucleic acid construct comprising AAVS1 (adeno-associated virus integration site, a safe harbor locus) arms that flank on both sides of the Tat gene and the reporter element for integration at the human AAVS1 site by homologus recombination. Further provided are methods of using a cell comprising the vector for studying the effects of exogenous conditions on expression of the Tat gene.

The present invention provides an expression cassette for reducing the risk of lentivirus integration, as well as its applications and products, belonging to the technical field of genetic engineering. The present invention is further optimized based on the prior art. The expression cassette is reversely assembled, and through the optimized selection of the polyA sequence, it is found that the vector of the present invention can improve the gene expression level of a single copy, achieve the same expression effect with a lower lentivirus integration copy number, thereby further reducing the risk brought by virus integration.

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.

The present invention relates to a method of identifying integrated viral DNA in the genome of at least one mammalian test cell, the method comprising the steps of: (a) determining the presence or absence of viral DNA in a DNA sample obtained from a mammalian test cell; and (b) determining the methylation status of at least one CpG site of the viral DNA in a DNA sample obtained from the mammalian test cell wherein the presence of the viral DNA after step (a) and the hypermethylation in step (b) respectively indicate that the viral DNA is integrated into the mammalian test cell and the virus is inactive; the existence of the virus DNA after the step (a) and the baseline methylation or hypomethylation in the step (b) respectively indicate that the virus DNA is integrated into the mammalian test cell, and the virus is active; and the absence of the viral DNA after step (a) indicates that the viral DNA is not integrated into the mammalian test cell, respectively; and wherein the method is performed on an array.

The present disclosure belongs to the field of molecular biology, particularly to the technical field of gene analysis and detection, and specifically relates to a method for preparing a DNA library and a method for detecting a retroviral integration site. Specifically, the method for preparing the DNA library comprises the following steps: 1) fragmenting a genomic DNA from a retrovirus-infected cell to obtain DNA fragments; 2) subjecting the DNA fragments to end-repair, A-tailing, and ligation with an adapter to obtain a ligation product, wherein the adapter is an asymmetric double-strand adapter comprising a long-strand sequence and a short-strand sequence, wherein the long-strand sequence sequentially comprises, from a 5′ end to a 3′ end, a fixed sequence, a random UMI sequence, and an amplification primer binding sequence, and the short-strand sequence comprises a sequence complementary to the fixed sequence; and other steps. The detection method of the present disclosure has extremely high sensitivity, thus having good application potential.