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Novel coronavirus variation analysis method and application

A coronavirus and mutation analysis technology, applied in the field of novel coronavirus mutation analysis, can solve the problems of high error rate of mutation detection, lack of new coronavirus mutation detection software, third-party general software cannot directly process metagenomic sequencing data, etc.

Active Publication Date: 2020-07-24
广州微远医疗器械有限公司 +3
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0006] In summary, there is currently a lack of mutation detection software developed for the new coronavirus, third-party general-purpose software cannot directly process metagenomic sequencing data, and the error rate of mutation detection is high

Method used

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  • Novel coronavirus variation analysis method and application
  • Novel coronavirus variation analysis method and application

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0060] A novel coronavirus (2019-nCoV) variation analysis method, comprising the following steps:

[0061] 1. Database construction

[0062] 1. Host database construction

[0063] Download the human reference genome (accession number: GCF_000001405.39) from the NCBI website (https: / / ftp.ncbi.nlm.nih.gov / genomes), and use the bwa index software to construct an index file to obtain the host database.

[0064] 2. Construction of the Novel Coronavirus Reference Genome Database

[0065] Download the new coronavirus (2019-nCoV) reference genome from the NCBI website, the accession number is GCF_009858895.2, and download the corresponding annotation file in gtf format. Use the bwa index to construct a novel coronavirus reference genome database.

[0066] The gene coordinates of this new coronavirus reference genome are shown in the table below.

[0067] Table 1. Gene coordinate information of the new coronavirus

[0068]

[0069] Extract the gtf file gene coordinates, coding ...

Embodiment 2

[0139] Evaluation of the accuracy of novel coronavirus mutation detection.

[0140] The combination of GATK and snpEff software is the most commonly used method with high accuracy in the field of microbial variation detection and annotation, and is called a classic method by the industry.

[0141] In order to evaluate the accuracy of the method of the present invention in detecting the mutation of the new coronavirus, it is most reasonable to analyze the virus with known mutation information. Therefore, this example will evaluate the present invention by comparing the variation detection results of the classical method and the method of the present invention accuracy of the method.

[0142] The above-mentioned classical method and the method of the present invention are used to analyze the sequencing data of the same known virus variation information.

[0143] The mutation information of the virus is shown in Table 6 below. There are 8 mutation sites in total, all of which ar...

Embodiment 3

[0153] Dynamic monitoring of novel coronavirus mutations.

[0154] This example will use simulated data to illustrate the application of the present invention in the dynamic monitoring of novel coronavirus mutations.

[0155] The duration of a patient infected with the new coronavirus is generally 14 days. A simulated continuous sampling of a patient with new coronary pneumonia for 14 days obtained 14 samples, which were named day1~day14 according to the order of time collection, and metagenomic sequencing was performed to detect the mutation of the new coronavirus. The method of Example 1 analyzes the dynamic process of variation.

[0156] Test results such as figure 2 shown. The results showed that 3 mutations were detected in 14 consecutive samples, namely orf1a:p.L1579R, N:p.G243V, and S:p.C480Y.

[0157] On day1 and day2, there was only one mutation, orf1a:p.L1579R, and the ratio was close to 1. A new mutation N:p.G243V appeared from day3, and a new mutation S:p.C480Y a...

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Abstract

The invention relates to a novel coronavirus variation analysis method and application, and belongs to the technical field of gene sequencing analysis. The method comprises the steps of data acquisition, data filtering, data comparison, variation detection, coordinate analysis, coordinate correction and variation annotation. According to the method, variation detection can be carried out on pure virus culture sequencing data, variation detection can also be carried out on metagenome sequencing data, and the application range is wider; and meanwhile, ribosome transcoding can be accurately annotated, and joint mutation can be accurately annotated, so that the mutation detection accuracy is improved; and in addition, the virus variation can be dynamically monitored.

Description

technical field [0001] The invention relates to the technical field of gene sequencing analysis, in particular to a novel coronavirus variation analysis method and application. Background technique [0002] The novel coronavirus (2019-nCoV) is a single-stranded positive-sense RNA virus that is prone to mutation. Clinically, the symptoms of patients infected with the new coronavirus vary widely, ranging from asymptomatic to critically ill. In addition to differences in individual factors, virus variation may also be an important factor leading to large differences in symptoms among infected patients. [0003] Studies have shown that the mutation rate of the new coronavirus is about 2 to 4 mutations per month, and more than 25 mutant strains have been found in known strains. The mutation of the virus will significantly affect its transmissibility and pathogenicity, and even drug resistance will increase the difficulty of treatment. Therefore, the monitoring of virus mutatio...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B30/10
CPCG16B30/10
Inventor 许腾陈文景曾伟奇刘足李永军王小锐苏杭
Owner 广州微远医疗器械有限公司
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