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MNP marker site of varicella-zoster virus, primer composition, kit and application of MNP marker site

A technology of herpes zoster virus and primer combination, applied in the biological field, can solve the problems of small number, insufficient to capture allelic diversity, huge number of SNP markers, etc., and achieve the effect of high-sensitivity detection and high-accuracy detection

Pending Publication Date: 2022-07-26
JIANGHAN UNIVERSITY
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

SSR markers are recognized as the most polymorphic markers, but their number is small in microorganisms; the number of SNP markers is huge, densely distributed, and they are dimorphic markers, and the polymorphism of a single SNP marker is not enough to capture potential alleles in microbial populations genetic diversity

Method used

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  • MNP marker site of varicella-zoster virus, primer composition, kit and application of MNP marker site
  • MNP marker site of varicella-zoster virus, primer composition, kit and application of MNP marker site
  • MNP marker site of varicella-zoster virus, primer composition, kit and application of MNP marker site

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0040] Example 1. Screening of varicella-zoster virus MNP marker sites and design of multiple PCR amplification primers

[0041] S1. Screening of varicella-zoster virus MNP marker sites

[0042] Based on the complete or partial genome sequences of 3794 different varicella-zoster virus isolates published on the Internet, 15 MNP marker sites were obtained by sequence alignment. For species for which there is no genome data online, the genome sequence information of the representative race of the microbial species to be detected can also be obtained by high-throughput sequencing, where the high-throughput sequencing can be whole genome or simplified genome sequencing. In order to ensure the polymorphism of the selected marker, the genome sequences of at least 10 genetically representative isolates are generally used as a reference. The 15 MNP marker sites screened are shown in Table 1:

[0043] Table 1 - The MNP marker site and the starting position of the detection primer on t...

Embodiment 2

[0055] Threshold setting and performance evaluation for the identification of varicella-zoster virus by MNP sites and primers described in Example 2

[0056] In this example, varicella-zoster virus nucleic acid standards with known copy numbers were added to human genomic DNA to prepare varicella-zoster virus simulations with 1 copy / reaction, 10 copies / reaction and 100 copies / reaction sample. At the same time, an equal volume of sterile water was set as a blank control. A total of 4 samples were collected, and 3 replicate libraries were constructed for each sample every day, and were continuously detected for 4 days, that is, 12 sets of sequencing data were obtained for each sample, as shown in Table 2. According to the number of sequencing fragments and loci of the varicella-zoster virus MNP locus detected in the blank control and varicella-zoster virus nucleic acid standard in 12 repeated experiments, the quality control system contamination and target pathogens were formul...

Embodiment 3

[0078] Example 3. Detection of genetic variation among varicella-zoster virus strains

[0079] Six varicella-zoster virus strains provided by Hubei Provincial Center for Disease Control and Prevention were detected using the described kit and MNP marker site detection method. -2 to S-5 are the progeny strains of the same strain in different periods. The average sequencing coverage of each sample was 2034-fold, and all 15 MNP markers could be detected for each strain (Table 5). The fingerprints of the 6 strains were compared in pairs, and the results are shown in Table 5. There are differences between S1 and other strains in at least 3 major genotypes of MNP sites; S-2 and S3-S5 also have differences. There were major genotypic differences at one MNP locus (Table 5), indicating strain-to-strain variation among strains of the same name.

[0080] Table 5-6 Detection and Analysis of Varicella-Zoster Viruses

[0081]

[0082] As can be seen from Table 5, the test kit of the p...

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Abstract

The invention discloses MNP marker sites of a varicella-zoster virus, a primer composition, a kit and application of the MNP marker sites, the primer composition and the kit, and the MNP marker sites refer to genome regions which are screened on a varicella-zoster virus genome, are distinguished from other species and have a plurality of nucleotide polymorphisms in the species, and comprise marker sites of MNP-1 to MNP-15; the primers are as shown in SEQ ID NO. 1 to SEQ ID NO. 30. The MNP marker site can be used for specifically identifying the varicella-zoster virus and monitoring variation; the primers do not interfere with each other, integrate multiple amplification and sequencing technologies, can perform sequence analysis on all marker sites of multiple samples at one time, have the detection advantages of high throughput, multiple targets, high sensitivity, high precision and no culture, can be applied to identification and heritable variation detection of varicella-zoster viruses of large-scale samples, and have broad application prospects. The method has important significance on scientific research and epidemic prevention monitoring of the varicella-zoster virus.

Description

technical field [0001] The embodiments of the present invention relate to the field of biotechnology, and in particular, to an MNP marker site of varicella-zoster virus, a primer composition, a kit and applications thereof. Background technique [0002] Varicella-zostervirus, human herpesvirus type 3 (HHV-3), is the causative agent of varicella or shingles. The varicella-zoster virus is very common. It enters the body through respiratory tract or contact infection through droplets. Almost all people have been exposed to the virus before adulthood. The virus has only one serotype and can cause two different symptoms, the primary infection. Chickenpox (varicella) and recurrent infections with herpes zoster (zoster). After the chickenpox disappears, no scar is left, and the disease is generally mild, but occasionally complicated with interstitial pneumonia and post-infectious encephalitis. When adults suffer from chickenpox, 20% to 30% of them are complicated with pneumonia. ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/70C12Q1/6858C12N15/11
CPCC12Q1/705C12Q1/6858C12Q2600/156C12Q2600/16C12Q2600/166C12Q2531/113C12Q2537/143C12Q2535/122C12Q2537/165C12Q2545/113
Inventor 李论彭海陈利红周俊飞李甜甜肖华锋高利芬方治伟
Owner JIANGHAN UNIVERSITY
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