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An automated method for detecting reassortment of segmented RNA viruses

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: 2021-05-18
ACADEMY OF MILITARY MEDICAL SCI
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  • Summary
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  • Description
  • Claims
  • Application Information

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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 different segments are also very different. Simply concatenating each segment to construct an evolutionary tree will produce an unreasonable genome evolution relationship, resulting in wrong reassortment detection results

Method used

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  • An automated method for detecting reassortment of segmented RNA viruses
  • An automated method for detecting reassortment of segmented RNA viruses
  • An automated method for detecting reassortment of segmented RNA viruses

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0042]Example 1, virus reassurance detection method

[0043]I. Preparation of the specific classification of each segment after the release

[0044]For the same variety of virus strains, the method of detecting the virus is included in the following steps:

[0045]1. Build a viral genome segment database

[0046]The genomic nucleic acid sequence of all intact genomics and the genomic nucleic acid sectors of the same virus strain are obtained from the database.

[0047]The sequence of each segment of the genomic nucleic acid sequence of different virus strains is used to perform multi-sequence alignment to obtain a multi-segment alignment result of each of the versions of all virus strains, which is recorded as a viral genome segment database.

[0048]2, build system development trees

[0049]The multi-segment comparison result of each of the versions of all virus strains obtained in step 1 is constructed by system development trees by maximum likelihood method, and the system development tree of each se...

Embodiment 2

[0077]Example 2, influenza virus reassurance detection

[0078]1, download the gisaid website to download the full influenza virus genome sequence data

[0079]Log in to gisaid (http: / / platform.gisaid.org), filtering the downloading of the hypertrophic virus genome nucleic acid sequence containing a complete genome and full length sequence, generates download files, downloading each influenza virus genome sequence data; There is also a genome such as a genome such as illegal characters, and delete the redundant genome.

[0080]In this embodiment, the full influenza genome sequence data downloaded in the Gisaid website database in 2016-10-26, with a total of 18,564 viral genome after data quality control.

[0081]The sequence of each segment of the genomic algorithm sequence of different virus strains utilizes the MAFFT software for multi-sequence alignment to obtain a multi-segment alignment result of each of the versions of all virus strains, which is recorded as a viral genome segment databas...

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Abstract

The invention discloses a method for automatically detecting segmented RNA virus reassortment. The invention provides a method for detecting virus reassortment based on the evolutionary relationship of each segment phylogenetic tree of the virus, comprising the following steps: 1) establishing a phylogenetic tree of each segment of the virus; The phylogenetic tree is clustered and divided based on the average pairwise distance, and the division class redefinition of each segment of each strain is obtained; 3) According to this definition, the reassortment history detection of virus strains can be realized, and for new strains The corresponding reassortment detection can be performed according to the segmental similarity. The experiment of the present invention proves that the present invention can detect the reassortment of virus strains without splicing and comparison of each segment through the clustering division of the evolutionary tree, and the detection result is reasonable and efficient.

Description

Technical field[0001]The present invention relates to the field of biotechnology, and more particularly to a method of automatically detecting a segment-segment RNA virus.Background technique[0002]REASORTMENT is a process of recombinant, which is unique to the segment RNA virus, refers to a plurality of viruses infected with the same host cell, due to the viral gene segment to produce new gene combination The phenomenon of future generations. The most typical influenza virus is detected in almost all of the segment viral families. Reinforcing an influenza virus to achieve an important evolutionary driving force that transfers across hosts or forms large-scale popularity. For example, viruses can quickly obtain critical loci mutations across host barriers, while simultaneously obtaining these host labels require a long evolution process. Multi-influenza epidemics in human history is related to the reinforcing between different viruses.[0003]Although recombination involves a recombina...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B40/00G16B30/10
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
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