Pathogenic microorganism analysis and identification system and application thereof

A technology of pathogenic microorganisms and species, applied in the field of pathogenic microorganism analysis and identification system, can solve the problems of inability to identify and detect pneumonia, unknown accuracy, rapid virus mutation, etc., and achieve the effect of improving detection accuracy, improving accuracy, and shortening analysis time

Active Publication Date: 2020-07-28
广州微远医疗器械有限公司 +3
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Conventional PCR kits can detect new coronaviruses quickly, but the virus mutates quickly, which can easily lead to PCR detection failure, and the current PCR kits on the market cannot perform multiple detections, that is, they cannot detect new coronavirus infections and non-new coronaviruses. Pneumonia caused by coronavirus infection is used for differential detection, and it is even more impossible to detect mixed infections
[0006] In addition, the current common metagenomics analysis method is not developed for the new coronavirus, and the database does not even contain the genome of the new coronavirus, so it is impossible to identify the new coronavirus
Even if the new coronavirus genome is added, the ordinary analysis process takes a long time, cannot be quickly identified, and the accuracy is unknown

Method used

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  • Pathogenic microorganism analysis and identification system and application thereof
  • Pathogenic microorganism analysis and identification system and application thereof
  • Pathogenic microorganism analysis and identification system and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0070] The establishment of pathogenic microorganism genome database, the process is as follows figure 1 shown.

[0071] 1. Genome collection

[0072] Collect representative genomes of pathogenic microorganisms and human reference genomes.

[0073] 1. Host library construction

[0074] Download the human reference genome (accession number: GCF_000001405.39) from the NCBI website, name it IDhost, and use the bwa software to construct an index file to obtain the available host library file, which is the host genome database.

[0075] 2. Microbial genome data download

[0076] Download all genomes classified as "bacteria", "fungi", "viral", "archaea", "protozoa" in the NCBI RefSeq genome (https: / / ftp.ncbi.nlm.nih.gov / genomes / refseq) database.

[0077] Each species may have multiple genome sequences. For species with multiple genome sequences, select the genome sequence marked as "reference genome" or "representative genome" as the reference genome of the species. For example...

Embodiment 2

[0089] A pathogenic microorganism analysis and identification system, such as figure 2 shown, execute the following procedure.

[0090] 1. Data acquisition

[0091] A gene sequencing off-machine data was obtained from the 2019 novel coronavirus standard sample (sourced from the Central Inspection Institute). The sequencing parameters were single-end sequencing and the read length was 75bp, which was used for the identification and analysis of the novel coronavirus.

[0092] The standard product is made by mixing 2019 novel coronavirus pseudovirus particles and human HeLa cells at a certain concentration, and the species information contained in it is shown in the table below.

[0093] Table 1. Microorganisms included in the standard

[0094] Latin name Chinese name Remark 2019-nCoV 2019 Novel Coronavirus target pathogen Mycoplasma hyorhinis Mycoplasma hyorhinosum HeLa Cell Culture Contaminants Human papillomavirus type 18 Human papillo...

Embodiment 3

[0122] In the field of metagenomic sequencing species classification and identification, the results obtained by comparing the BLAST software to the NCBI Nucleotide database (hereinafter referred to as the BLAST method) are usually referred to as the "gold standard" in the industry. In order to evaluate the analytical performance of the method of the present invention, the method of the present invention will be compared with the conventional BLAST software analysis method in terms of analysis time and accuracy, so as to illustrate the advantages of the method of the present invention in analysis time and accuracy.

[0123] 1. Data source

[0124] In order to avoid the interference of unknown factors, this assessment is carried out using the method of simulated data. 100,000 sequences of length 75 were randomly extracted from the genomes of 16 common pathogens to generate simulated FASTQ files. The 16 pathogens include 8 viruses, 4 bacteria and 4 fungi, which can be evaluated...

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Abstract

The invention relates to a pathogenic microorganism analysis and identification system and application thereof, and belongs to the technical field of gene detection and analysis. The pathogenic microorganism analysis and identification system comprises: a data acquisition module used for acquiring gene sequencing data obtained by high-throughput sequencing; a data filtering module used for performing low-quality sequence filtering and host sequence filtering in sequence; a data comparison module used for comparing sequences to a pathogenic microorganism genome database; a species comparison module used for counting to-be-analyzed sequences; a data analysis module used for calculating the similarity S and the average similarity value SMSi of each species on each sequence comparison in the common comparison sequence set; a species sequence module used for calculating the total comparison sequence number SNTi of the species; and a result output module used for carrying out bioinformaticsanalysis to obtain a pathogenic microorganism analysis and identification result. The pathogenic microorganism analysis and identification system has the advantages of short analysis time and high accuracy, and can accurately detect mixed infection and obtain specific pathogen information.

Description

technical field [0001] The invention relates to the technical field of gene detection and analysis, in particular to a pathogenic microorganism analysis and identification system and its application. Background technique [0002] The novel coronavirus was first discovered and identified by the metatranscriptome sequencing technology. The bioinformatics analysis of the metatranscriptome is an extremely critical step. The performance of the bioinformatics analysis determines whether it can be analyzed and identified accurately and quickly. Novel coronavirus. [0003] The performance of bioinformatics analysis is mainly determined by two aspects: analysis timeliness and accuracy of analysis results. Being able to quickly and accurately identify the new coronavirus can effectively help doctors speed up the investigation of suspected cases, and admit and treat confirmed patients as soon as possible, which plays a great role in the control of the epidemic. [0004] The outbreak ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B30/00
CPCG16B30/00
Inventor 许腾陈文景张丽珍刘足潘秀莹曾伟奇秦璐李永军王小锐苏杭
Owner 广州微远医疗器械有限公司
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