TY - GEN
T1 - Evidence of Increased Adaptation of Omicron SARS-CoV-2 Codons to Humans
AU - Davidson, Alma
AU - Parr, Marina
AU - Totzeck, Franziska
AU - Churkin, Alexander
AU - Barash, Danny
AU - Frishman, Dmitrij
AU - Tuller, Tamir
N1 - Publisher Copyright:
© The Author(s), under exclusive license to Springer Nature Switzerland AG 2024.
PY - 2024
Y1 - 2024
N2 - Viruses are highly dependent on their hosts to carry out cellular mechanisms and cause productive infection. Thus, they undergo extensive adaptations to the host intracellular machinery, which occur over the evolution of the virus, and during the emergence of new viral strains with different properties. One aspect of viral adaptation is related to the efficiency of recruiting the host’s gene expression machinery and specifically the translation machinery. This process can be partially detected using measures of codon usage bias (CUB). While previous studies in the field suggested that there is an adaptation of codons in the viral genome to the host, none of them studied these adaptations among the different strains of the same virus over time. Thus, in this study, we focused on the SARS-CoV-2 and demonstrated for the first time that the omicron strain has an increased codon usage adaptation to humans in the early gene ORF1ab compared to previous strains. In addition, our findings indicate that the observed differences in CUB scores were primarily attributed to non-synonymous mutations. This conclusion holds for additional human-infecting viruses.
AB - Viruses are highly dependent on their hosts to carry out cellular mechanisms and cause productive infection. Thus, they undergo extensive adaptations to the host intracellular machinery, which occur over the evolution of the virus, and during the emergence of new viral strains with different properties. One aspect of viral adaptation is related to the efficiency of recruiting the host’s gene expression machinery and specifically the translation machinery. This process can be partially detected using measures of codon usage bias (CUB). While previous studies in the field suggested that there is an adaptation of codons in the viral genome to the host, none of them studied these adaptations among the different strains of the same virus over time. Thus, in this study, we focused on the SARS-CoV-2 and demonstrated for the first time that the omicron strain has an increased codon usage adaptation to humans in the early gene ORF1ab compared to previous strains. In addition, our findings indicate that the observed differences in CUB scores were primarily attributed to non-synonymous mutations. This conclusion holds for additional human-infecting viruses.
KW - Codon usage bias
KW - Gene expression
KW - Genome evolution
KW - Genomic variation
KW - SARS-CoV-2
UR - http://www.scopus.com/inward/record.url?scp=85192258207&partnerID=8YFLogxK
U2 - 10.1007/978-3-031-58072-7_13
DO - 10.1007/978-3-031-58072-7_13
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AN - SCOPUS:85192258207
SN - 9783031580710
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 248
EP - 270
BT - Comparative Genomics - 21st International Conference, RECOMB-CG 2024, Proceedings
A2 - Scornavacca, Celine
A2 - Hernández-Rosales, Maribel
PB - Springer Science and Business Media Deutschland GmbH
T2 - 21st RECOMB International Workshop on Comparative Genomics, RECOMB-CG 2024
Y2 - 27 April 2024 through 28 April 2024
ER -
