AI-based search for convergently expanding, advantageous mutations in SARS-CoV-2 by focusing on oligonucleotide frequencies

Among mutations that occur in SARS-CoV-2, efficient identification of mutations advantageous for viral replication and transmission is important to characterize and defeat this rampant virus. Mutations rapidly expanding frequency in a viral population are candidates for advantageous mutations, but n...

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Bibliographic Details
Published in:PloS one 2022-08, Vol.17 (8), p.e0273860-e0273860
Main Authors: Ikemura, Toshimichi, Iwasaki, Yuki, Wada, Kennosuke, Wada, Yoshiko, Abe, Takashi
Format: Article
Language:English
Subjects:
Amino acids
Analysis
Artificial intelligence
Biology and Life Sciences
Convergence
Coronaviruses
COVID-19
Disease transmission
Gene mutations
Gene sequencing
Genomes
Medicine and health sciences
Mutation
Oligonucleotides
Pandemics
Phylogeny
Population
Proteins
Severe acute respiratory syndrome
Severe acute respiratory syndrome coronavirus 2
Viral diseases
Viruses
Zoonoses
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Summary:Among mutations that occur in SARS-CoV-2, efficient identification of mutations advantageous for viral replication and transmission is important to characterize and defeat this rampant virus. Mutations rapidly expanding frequency in a viral population are candidates for advantageous mutations, but neutral mutations hitchhiking with advantageous mutations are also likely to be included. To distinguish these, we focus on mutations that appear to occur independently in different lineages and expand in frequency in a convergent evolutionary manner. Batch-learning SOM (BLSOM) can separate SARS-CoV-2 genome sequences according by lineage from only providing the oligonucleotide composition. Focusing on remarkably expanding 20-mers, each of which is only represented by one copy in the viral genome, allows us to correlate the expanding 20-mers to mutations. Using visualization functions in BLSOM, we can efficiently identify mutations that have expanded remarkably both in the Omicron lineage, which is phylogenetically distinct from other lineages, and in other lineages. Most of these mutations involved changes in amino acids, but there were a few that did not, such as an intergenic mutation.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0273860