Method for automatically detecting reassortment of segmental RNA (Ribonucleic Acid) virus

A technology of segments and viruses, applied in the field of automatic detection of segmented RNA virus reassortment, can solve problems such as wrong reassortment detection results, unreasonable genome evolution relationship, etc. The method is simple and effective, the detection speed is fast, and unreasonable avoidance Effects of Sex and Complexity

Active Publication Date: 2018-11-20
ACADEMY OF MILITARY MEDICAL SCI
View PDF5 Cites 0 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

In fact, there are large differences in the evolution of different segments of segmented viruses. On the one hand, the selection pressures on different segments are different, and on the other hand, the evolution rates of

Method used

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • Method for automatically detecting reassortment of segmental RNA (Ribonucleic Acid) virus
  • Method for automatically detecting reassortment of segmental RNA (Ribonucleic Acid) virus
  • Method for automatically detecting reassortment of segmental RNA (Ribonucleic Acid) virus

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0042] Embodiment 1, virus reassortment detection method

[0043] 1. The preparation of the phylogenetic tree of the specific classification of each segment after the labeling

[0044] For multiple virus strains of the same species, the method for detecting virus reassortment comprises the following steps:

[0045] 1. Construction of viral genome segment database

[0046] Obtain all genome nucleic acid sequences of the same virus with complete genomes and full-length sequences from the database, and the segments of the genome nucleic acid sequences of the same virus strain are the same;

[0047] The sequences of each segment of the genome nucleic acid sequences of different virus strains are compared using software to obtain the multiple sequence alignment results of each segment of all virus strains, which are recorded as the viral genome segment database.

[0048] 2. Build a phylogenetic tree

[0049] The multiple sequence alignment results of each segment of all virus st...

Embodiment 2

[0077] Embodiment 2, influenza virus reassortment detection

[0078] 1. Download the complete influenza virus genome sequence data from the GISAID website

[0079] Log in to GISAID (http: / / platform.gisaid.org), screen and download influenza A virus genome nucleic acid sequences that contain a complete genome and have a full-length sequence, and generate a download file that contains each influenza virus genome sequence data; There are also genomes with low data quality such as illegal characters, and redundant genomes are deleted.

[0080] In this example, the complete influenza virus genome sequence data downloaded from the GISAID website database on 2016-10-26, a total of 18564 virus genomes after data quality control.

[0081] The sequence of each segment of the genome accounting sequence of different virus strains was compared using MAFFT software, and the multiple sequence alignment results of each segment of all virus strains were obtained, which was recorded as the vir...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to view more

PUM

No PUM Login to view more

Abstract

The invention discloses a method for automatically detecting reassortment of a segmental RNA (Ribonucleic Acid) virus and provides a method for performing virus reassortment detection based on an evolutionary relationship of a phylogenetic tree at each segment of the virus. The method comprises the following steps of (1) establishing the phylogenetic tree at each segment of the virus; (2) performing clustering division on the segmental phylogenetic trees obtained in the step (1) according to an average pairing distance to obtain a divided category redefinition for each segment of each virulentstrain; and (3) realizing reassortment history detection for the virulent strain of the virus according to the definition, and meanwhile performing corresponding reassortment detection according to asegmental similarity for new virulent strain data. Experiments prove that splicing comparison of each segment is not needed, the reassortment detection for the virulent strain of the virus can be implemented through clustering division of an evolutionary tree, and a detection result is reasonable and efficient.

Description

technical field [0001] The invention relates to the field of biotechnology, in particular to a method for automatically detecting segmented RNA virus reassortment. Background technique [0002] Virus reassortment (Reassortment) is a process of genetic recombination, which is unique to segmented RNA viruses, and refers to the co-infection of multiple viruses in the same host cell, resulting in a new gene combination due to the rearrangement of viral gene segments The phenomenon of progeny viruses. Reassortment was detected in almost all families of segmented viruses, most notably influenza A viruses. Reassortment is an important evolutionary force for influenza virus to achieve cross-host transmission or form a large-scale epidemic. For example, viruses can quickly acquire mutations at key sites that cross host barriers through reassortment, while acquiring these host markers simply through mutation accumulation requires a long evolutionary process. Many influenza outbreak...

Claims

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to view more

Application Information

Patent Timeline
no application Login to view more
IPC IPC(8): G06F19/18G06F19/20G06F19/22
Inventor 任洪广梁龙岳俊杰靳远黄志松周静胡明达彭小川周江林
Owner ACADEMY OF MILITARY MEDICAL SCI
Who we serve
  • R&D Engineer
  • R&D Manager
  • IP Professional
Why Eureka
  • Industry Leading Data Capabilities
  • Powerful AI technology
  • Patent DNA Extraction
Social media
Try Eureka
PatSnap group products

Browse by: Latest US Patents, China's latest patents, Technical Efficacy Thesaurus, Application Domain, Technology Topic.

© 2024 PatSnap. All rights reserved.Legal|Privacy policy|Modern Slavery Act Transparency Statement|Sitemap