Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura-Cho 1266, Nagahama-Shi, Shiga-Ken, 526-0829, Japan.
Department of Information Engineering, Graduate School of Science and Technology, Niigata University, Niigata-Ken, 950-2181, Japan.
Virol J. 2023 Mar 1;20(1):39. doi: 10.1186/s12985-023-01995-3.
Viruses use various host factors for their growth, and efficient growth requires efficient use of these factors. Our previous study revealed that the occurrence frequency of oligonucleotides in 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.
Herein, we compared the frequency of oligonucleotides in the genome of alpha- and betacoronavirus with those in the genomes of humans and bats, which are typical hosts of the viruses.
By comparing the oligonucleotide frequency in coronaviruses and their host genomes, we found a statistically tested 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.
In alpha- and betacoronaviruses, 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.
病毒利用各种宿主因子进行生长，而有效的生长需要有效地利用这些因子。我们之前的研究表明，流感病毒基因组中寡核苷酸的出现频率在不同的宿主中明显不同，并且这种频率往往会适应它们生长的宿主细胞。我们旨在研究一种人畜共患病毒对宿主细胞的适应机制。
在此，我们比较了甲型和乙型冠状病毒基因组中的寡核苷酸频率与人类和蝙蝠基因组中的寡核苷酸频率，蝙蝠是这些病毒的典型宿主。
通过比较冠状病毒和宿主基因组中的寡核苷酸频率，我们发现冠状病毒的频率与病毒来源的宿主的外显子区域的频率之间存在统计学上的正相关。为了研究假定伴随病毒从非人类宿主向人类宿主转变的早期病毒基因组变化特征，我们比较了大流行初期的严重急性呼吸综合征冠状病毒 2（SARS-CoV-2）和此后流行的变异体之间的寡核苷酸频率，发现向宿主外显子区域频率的变化。
在甲型和乙型冠状病毒中，基因组寡核苷酸频率被认为会响应病毒复制的细胞环境而发生变化，实际上频率已经接近宿主中外显子区域的频率。
