Oligonucleotide usage in coronavirus genomes mimics that in exon regions in host genomes

Abstract Background Viruses utilize various host factors for their growth, and efficient growth requires efficient utilization of these factors. Our previous study revealed that the occurrence frequency of oligonucleotides in the viral genome (e.g. the influenza virus genome) is distinctly different among derived hosts, and the frequency tends to adapt to the host cells in which they grow. We aimed to study the adaptation mechanisms of a zoonotic virus to host cells. Methods Herein, we compared the frequency of oligonucleotides in the coronavirus genome with those in the genomes of humans and bats, which are typical hosts of the virus. Results By comparing the oligonucleotide frequency in coronaviruses and their host genomes, we found a positive correlation between the frequency of coronaviruses and that of the exon regions of the host from which the virus is derived. To examine the characteristics of early-stage changes in the viral genome, which are assumed to accompany the host change from non-humans to humans, we compared the oligonucleotide frequency between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the beginning of the pandemic and the prevalent variants thereafter, and found changes towards the frequency of the host exon regions. Conclusions In coronaviruses, the genome oligonucleotide frequency is thought to change in response to the cellular environment in which the virus is replicating, and actually the frequency has approached the frequency in exon regions in the host.