Cluster Analysis of SARS-CoV-2 Gene using Deep Learning Autoencoder : Gene Profiling for Mutations and Transitions

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Author: Miyake, Junほか

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Publication date: 2021-03-16

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Note (General)：: We report on a method for analyzing the variant of coronavirus genes using autoencoder. Since coronaviruses have mutated rapidly and generated a large...

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Material Type: 文書・図像類
Title: Cluster Analysis of SARS-CoV-2 Gene using Deep Learning Autoencoder : Gene Profiling for Mutations and Transitions
Author/Editor: Miyake, Jun
Sato, Takaaki
Baba, Shunsuke
Nakamura, Hayao
Niioka, Hirohiko
Nakazawa, Yoshihisa
Author Heading: Miyake, Jun
Sato, Takaaki
Baba, Shunsuke
Nakamura, Hayao
Niioka, Hirohiko
Nakazawa, Yoshihisa
Publication Date: 2021-03-16
Publication Date (W3CDTF): 2021-03-16
Alternative Title: SARS-CoV-2 genome clusters analyzed by Deep Learning
Text Language Code: eng
Subject Heading: Autoencoder
Deep Learning
SARS-CoV-2
Genome
Mutation
Classification
Cluster
Target Audience: 一般
Note (General): We report on a method for analyzing the variant of coronavirus genes using autoencoder. Since coronaviruses have mutated rapidly and generated a large number of genotypes, an appropriate method for understanding the entire population is required. The method using autoencoder meets this requirement and is suitable for understanding how and when the variants emarge and disappear. For the over 30,000 SARS-CoV-2 ORF1ab gene sequences sampled globally from December 2019 to February 2021, we were able to represent a summary of their characteristics in a 3D plot and show the expansion, decline, and transformation of the virus types over time and by region. Based on ORF1ab genes, the SARS-CoV-2 viruses were classified into five major types (A, B, C, D, and E in the order of appearance): the virus type that originated in China at the end of 2019 (type A) practically disappeared in June 2020; two virus types (types B and C) have emerged in the United States and Europe since February 2020, and type B has become a global phenomenon. Type C is only prevalent in the U.S. and is suspected to be associated with high mortality, but this type also disappeared at the end of June. Type D is only found in Australia. Currently, the epidemic is dominated by types B and E.
Format (IMT): application/pdf
Source: http://repo.lib.tokushima-u.ac.jp/files/public/11/116298/20211104160231558648/biorxiv_20210316.pdf
http://repo.lib.tokushima-u.ac.jp/files/public/11/116298/20211104160231558648/biorxiv_20210316.pdf
Access Restrictions: 限定公開
Rights (production): The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Related Material (DOI): 10.1101/2021.03.16.435601
Data Provider (Database): 国立情報学研究所 : 学術機関リポジトリデータベース（IRDB）（機関リポジトリ）
https://irdb.nii.ac.jp
Original Data Provider (Database): 徳島大学 : 徳島大学機関リポジトリ