109 results about "Viral sequence" patented technology

The present invention relates to methods and compositions for the elucidation of mammalian gene function. Specifically, the present invention relates to methods and compositions for improved mammalian complementation screening, functional inactivation of specific essential or non-essential mammalian genes, and identification of mammalian genes which are modulated in response to specific stimuli.In particular, the compositions of the present invention include, but are not limited to, replication-deficient retroviral vectors, libraries comprising such vectors, retroviral particles produced by such vectors in conjunction with retroviral packaging cell lines, integrated provirus sequences derived from the retroviral particles of the invention and circularized provirus sequences which have been excised from the integrated provirus sequences of the invention. The compositions of the present invention further include novel retroviral packaging cell lines.

The invention is a method and device for collecting and processing a biological specimen for the analyses of nucleic acids. A device comprises a matrix to which cells and viruses adhere and a handle to manipulate the matrix. The devices are used to collect, dry, transport, store and process small amounts of blood or other tissue. The matrix of the device is transferred to a reaction tube and amplifying reagents added to it. Nucleic acid sequences and relative quantities are detected and analyzed from the same specimen. The relative amounts of amplified nucleic acid from one or more particular RNA sequences are compared to one another and to the amount of amplified nucleic acid from DNA sequences serving as an internal control for the number of biological units per specimen. The relative amounts of amplified viral sequences from suspected viruses in the biological specimen and from recombinant viral particles serving as a viral quantitation standard enable estimation of viral burden in a given quantity of specimen.

The present invention is directed to ancestral and COT nucleic acid and amino acid sequences, methods for producing such sequences and uses thereof, including prophylactic and diagnostic uses.

The present invention relates to systems, methods and kits for low-level detection of nucleic acids, detecting at least two different viral sequences in a single reaction vessel, and increasing the dynamic range of detection of a viral target nucleic acid in a sample. The present invention also relates to T-structure invasive cleavage assays, as well as T-structure related target dependent non-target amplification methods and compositions. The present invention further relates to methods, compositions, devices and systems for consistent nucleic acid dispensing onto surfaces.

The invention provides arrays and probes for resequencing a SARS virus using an array of probes that are complementary to a SARS reference sequence and to each possible single nucleotide substitution of the reference sequence. Methods of identifying mutations in viral sequences and methods of characterizing viral isolates are also provided. The invention also provides high throughput methods to monitor epidemics and pandemics caused by pathogens such as viruses.

Recombinant negative-strand viral RNA templates are described which may be used with purified RNA-directed RNA polymerase complex to express heterologous gene products in appropriate host cells and/or to rescue the heterologous gene in virus particles. The RNA templates are prepared by transcription of appropriate DNA sequences with a DNA-directed RNA polymerase. The resulting RNA templates are of the negative-polarity and contain appropriate terminal sequences which enable the viral RNA-synthesizing apparatus to recognize the template. Bicistronic mRNAs can be constructed to permit internal initiation of translation of viral sequences and allow for the expression of foreign protein coding sequences from the regular terminal initiation site, or vice versa.

The invention discloses a method and device for screening COVID-19 drugs. On the basis of obtaining sequence similarity information between viruses and structure similarity information between pharmaceutical chemical structures, a heterogeneous network based on virus sequence similarity and drug similarity is constructed, and training is performed on the constructed data set by using a random walkalgorithm so as to obtain a COVID-19 drug screening model. Based on the drug screening model, drugs related to new coronal pneumonia can be effectively screened. According to the method, the researchand development cost of the COVID-19 drugs can be reduced, and the screening speed and accuracy of the COVID-19 drugs exceed those of representative methods applied to other bioinformatics fields.

The present invention relates to methods for screening compounds that can inhibit the early stage of an infection by the HIV-1 virus, that is to say the initiation step of viral genome reverse transcription, before integrating viral sequences into the cellular genome of the infected host organism.

The invention relates to an RT-PCR detection method of an ordinary rice black streaked dwarf virus (RBSDV). A pair of used primers are obtained by the method that the first section of RNA of an RBSDV is specific, and nucleotide sequences of the first section of RNA of the RBSDV and the first section of RNA of similar viruses are researched and downloaded from NCBI by utilizing the conservative property of the evolution of viral nucleotide sequences; and the sequences are compared by using MEGA4.0 software to find out a primer candidate area which is reported by different researchers and shared by the RBSDV nucleotide sequences and is different from other viral sequences from a mas file. Proved by BLAST results, the sequences which can 100 percent cover the primer 1 and the primer 2 and 100 percent same as the primer 1 and the primer 2 are all the RBSDV nucleotide sequences. RBSDV and SRBSDV viruses can be exactly separated by using the pair of primers for carrying out RT-PCR detections on the RBSDV and SRBSDV viruses.

The present invention provides recombinant DNA constructs for inactivation of viral or endogenous genes in a cell, wherein the construct comprises viral sequence sufficient to activate RNA silencing. In another aspect, the invention provides methods for identifying RNA silencing suppressors by sequence analysis and functional tests. In yet another aspect, the invention provides a method for identifying inhibitors of RNA silencing suppressors. In still other aspects, the invention comprises methods for identifying genes in the antiviral RNA silencing pathway, enhancers of the antiviral pathway, and methods of treating or preventing viral infections using enhancers of the pathway.

Methods are described for predicting ancestral sequences for viruses or portions thereof. Also described are predicted ancestral sequences for adeno-associated virus (AAV) capsid polypeptides. The disclosure also provides methods of gene transfer and methods of vaccinating subjects by administering a target antigen operably linked to the AAV capsid polypeptides.

Disclosed herein are new defective Sindbis viral vectors made from a novel Helper plasmid, with differences in envelope proteins between JT vectors and consensus Sindbis virus sequences, and also between JT and Ar-339 vectors. Also disclosed are vectors produced using the plasmid, methods for producing the vectors, methods for treating mammals suffering from tumors and pharmaceutical formulations for use in the treatment methods.

The invention relates to a method for cultivating tobacco capable of resisting various viruses by adopting an RNAi (RNA interference) technique. The method comprises the following steps of: obtaining relatively conservative areas of four kinds of viruses within a genome range through screening by comparing full-length sequences of multiple genomes of four kinds of viruses, i.e. CMV (cucumber mosaic virus), PVY (potato virus Y), PVX (potato virus X) and TMV (tobacco mosaic virus) in a genBank; selecting virus sequences and artificially synthesizing 800bp mosaic genes; and accordingly constructing RNAi plant expression carriers of the mosaic genes and transforming common tobacco through agrobacterium to obtain transgenic plants. The method for cultivating tobacco capable of resisting various viruses by adopting the RNAi technique has the characteristics that the four kinds of major tobacco viruses in China are selected as targets, the artificially constructed hairpin structures comprising the sequences of the four kinds of viruses are transformed into the tobacco by using the plant genetic engineering technique, a hairpin double-strand RNA structure transcribed by the tobacco is cut into siRNA (small interfering RNA) by the plant self mechanism, the normal duplication and the accumulation of target virus genes in tobacco plants are specifically interfered, degraded or silenced, and new tobacco materials capable of resisting various viruses can be obtained through screening.

The invention relates to a fluorescent quantitative detection kit for simultaneously detecting human influenza A virus, human influenza B virus and novel coronavirus, and belongs to the technical field of nucleic acid detection. The detection kit specifically comprises four groups of specific primer pairs and probes, a negative quality control material, a positive quality control material and a fluorescent quantitative PCR reaction system, wherein the four groups of specific primer pairs and probes are respectively a pair of specific primers and a probe for detecting influenza A virus and influenza B virus, and two pairs of specific primers and two probes for detecting novel coronavirus; wherein the positive quality control material is an artificially synthesized target sequence, and the negative quality control material is deionized water; wherein the fluorescent quantitative PCR reaction system is composed of components for PCR reaction and reaction conditions. According to the kit disclosed by the invention, the specific primer pair and the probe are designed at a conservative site of a virus sequence; the kit can realize simultaneous detection of influenza A virus, influenza Bvirus and novel coronavirus in a single tube, has strong detection specificity and high sensitivity, and can accurately and rapidly distinguish influenza from new coronapneumonia patients from people,so as to realize early discovery, early isolation and early treatment. The kit has important application value in the fields of disease monitoring, clinical diagnosis and the like.

The invention belongs to the field of virus detection and discloses a crucian carp bafinivirus HB93, RT-PCR detection primers and applications of the bafinivirus and the primers. The crucian carp bafinivirus is separated from crucian for the first time by the inventor, and is the crucian carp bafinivirus HB93. The primers are designed for the sequence of the virus and include F1 that is 5'-CAAAGTAAACCCTGGAGA-3', R1 that is 5'-ATCAATGATGGTGCAGTT-3', F2 that is 5'-TGAAACAATCCAAGAAGA-3' and R2 that is 5'-ACAAGTTATAGCCGGTGT-3. The primers can be used for detecting the crucian carp bafinivirus, and have high specificity and high sensitivity.

The invention provides a transcriptome sequencing method for microviridae and geminivirus viral genome splice. The method comprises the three steps of performing transcriptome sequencing on an infected DNA virus sample, comparing and splicing viral sequences and filling a blank area of the viral genome sequence. According to the method provided by the invention, the whole genome sequence of the banana bunchy top virus can be acquired and the other microviridae or geminivirus viral genomes can be spliced so as to acquire the whole genome sequence of the virus. The invention firstly reports the method for sequencing the spliced DNA viral genome in high throughput by utilizing transcriptome at home and abroad and fills the blank of the field at home and abroad. The method provided by the invention can be used for identifying and detecting DNA virus.

Described are single-stranded new sequences of TT viruses, rearranged TTV sequences and hybrid molecules of a specific TT virus sequence and host cell DNA that are capable of replicating autonomously for use in diagnosis, prevention and treatment of diseases like cancer and autoimmunity. In addition, it relates to the use of such molecules as gene vectors and artificial chromosomes.

The invention discloses a novel coronapneumonia virus rapid detection test strip and application thereof, and belongs to the field of biotechnology detection. Specifically, the novel coronapneumonia virus is firstly combined with an immobilized N95-like membrane with ACE2 receptor activity; an ACE2 receptor-virus-probe trimolecular compound is formed by adding a specific probe with complementary virus RNA sequences, and due to the fact that a chromogenic reagent is marked on the probe, chromogenic means that viruses are positive, and non-chromogenic means that viruses are negative. The kit hasthe characteristics of simpleness, rapidness, no need of blood drawing, capability of realizing home or field detection, specificity, sensitivity, no need of auxiliary reagents and instruments, result observation by naked eyes and the like, and becomes the fastest, simplest and most convenient novel coronapneumonia virus detection technology at present.

The invention relates to an RT-PCR detection method of a south rice black-streaked dwarf virus (SRBSDV). In the detection method, SRBSDV specific primers are used for carrying out RT-PCR amplification on a sample to be detected and then carrying out electrophoretic identification. The specific primers are obtained by the method that by utilizing the conservatism of the evolution of viral nucleotide sequences, the tenth section of RNA of SRBSDV and nucleotide sequences of the tenth section of RNA of similar viruses are searched and downloaded from NCBI/GenBank, the sequences are compared by utilizing MEGA4.0 software, and then a pair of primers which are shared by all the SRBSDV nucleotide sequences reported by different researchers and are different from other viral sequences are found out from a file with an extension name of mas. Proved by a BLAST result, sequences which 100 percent cover the primers and 100 percent same as the primers are all the SRBSDV nucleotide sequences. The primers can be used for accurately separating SRBSDV diseased plants from ordinary RBSDV diseased plants without a nested RT-PCR detection.

The invention discloses a method for detecting a macro virus group in a sample, and belongs to the technical field of metagenome analys.The method comprises the steps that second-generation sequencing data and third-generation sequencing data of a to-be-detected sample are mutually corrected and mixed and assembled to obtain mixed and assembled contigs, and the third-generation sequencing data are independently assembled to obtain Nanopore contigs; further, the mixed assembly contigs and the Nano-virus contigs are respectively subjected to comparison and annotation, so that candidate virus contigs, non-virus contigs and Nano-virus contigs are obtained, and the candidate virus contigs, the non-virus contigs and the Nano-virus contigs are subjected to comparison and annotation; and finally, carrying out clustering analysis on the three data sets, carrying out further comprehensive analysis according to a clustering result, supplementing missing virus sequences, and correcting a species annotation result to obtain a more sensitive, accurate and comprehensive virus identification result.

The present invention concerns a method of genetic modification of a TGB-3 wild type viral sequence for reducing or suppressing the possible deleterious effects of the agronomic properties of a transformed plant or plant cell by said TGB-3 viral sequence, comprising the following successive steps: submitting said sequence to point mutation(s) which allow the substitution of at least one amino-acid into a different amino-acid; selecting genetically modified TGB-3 wild type viral sequences having said point mutation(s) and which are not able to promote cell-to-cell movement of a mutant virus having a dysfunctional TGB-3 wild type viral sequence, when expressed in trans from a replicon; further selecting among said genetically modified TGB-3 viral sequences, the specifically genetically modified sequence which inhibits infection with a co-inoculated wild type virus when the mutant form was expressed from a replicon, and recovering said specifically genetically modified TGB-3 viral sequence. The invention further relates to genetically modified TGB-3 viral sequences suitable to induce gene silencing. In particular hairpin constructs based on such sequences proved highly efficient to induce a PTGS mechanism and degradation of the whole of RNA2 thereby. When plants are transformed accordingly the spread of the virus in the plant is significantly reduced or blocked.

The invention belongs to the virus detection field, in particular, discloses a Chinese rice virus-Field eel rhabdovirus Cr-ERV and RT-PCR detection primer and an application thereof. The Monopterus albus rhabdovirus is isolated from diseased Monopterus albus seedlings, and the virus is (Chinese rice virus-Field eel rhabdovirus) CrERV, deposited as CCTCC NO: V201819, is of pioneering significance for the study of Monopterus albus rhabdovirus. Primers are designed to detect rhabdovirus of Monopterus albus. The primers have good specificity and high sensitivity.

The invention relates to a coronavirus sequence recognition method based on a gated recurrent unit neural network. The coronavirus sequence recognition method comprises the following steps: S1, collecting data; S2, preprocessing the collected data, and performing data extraction from an original training sample to obtain a training set, a verification set and a test set; establishing an independent test set based on coronavirus sequences; S3, encoding each data set obtained in the S2, and establishing a classification model for training coronavirus sequences; S4, correcting the model; S5, counting an output score of the model to each sequence of a test set after the coronavirus sequence and the human genome sequence are merged; S6, setting a rejection interval according to the distributioncondition of the output score so as to reduce errors; S7, when the output score is larger than or equal to the upper limit threshold value of the rejection interval, judging the sequence to be a coronavirus sequence; and when the output score is less than or equal to the lower limit threshold of the rejection interval, judging that the sequence is a human genome sequence.