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ID 116298
Title Alternative
SARS-CoV-2 genome clusters analyzed by Deep Learning
Author
Miyake, Jun Osaka University
Sato, Takaaki Osaka University
Baba, Shunsuke Osaka University
Nakamura, Hayao Osaka University
Niioka, Hirohiko Osaka University
Keywords
Autoencoder
Deep Learning
SARS-CoV-2
Genome
Mutation
Classification
Cluster
Content Type
Preprint
Description
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.
Published Date
2021-03-16
Remark
This article is a preprint and has not been certified by peer review.
Rights
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.
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DOI (Published Version)
URL ( Publisher's Version )
FullText File
language
eng
TextVersion
Author
departments
Bioscience and Bioindustry