Phakaratsakul Supinya, Sirihongthong Thanyaporn, Boonarkart Chompunuch, Suptawiwat Ornpreya, Auewarakul Prasert
Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
Research and International Relations Division, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand.
Arch Virol. 2018 Oct;163(10):2883-2888. doi: 10.1007/s00705-018-3930-7. Epub 2018 Jul 9.
RNA viruses are classified by their genome polarity and replication strategies. Nucleotide composition and codon usage differ among virus groups, for instance positive-sense RNA (+ssRNA) viruses have higher GC-content than the other RNA virus groups. Codon usage of +ssRNA viruses is closer to humans showing significantly higher codon adaptation index (CAI) than those of negative-sense RNA (-ssRNA), double stranded RNA (dsRNA) and retroviruses. Ambisense viruses have high CAI comparable to that of +ssRNA virus despite their lower GC content, whereas dsRNA viruses have the lowest CAI. This may provide a benefit for +ssRNA viruses as their genomes are used as mRNA. However, analyses for influence of nucleotide composition on codon usage did not show a difference between +ssRNA and -ssRNA viruses. This suggests that genome composition and hence mutational pressure remain the major pressure causing the differences in codon usage among RNA viruses with different genome types.
RNA病毒根据其基因组极性和复制策略进行分类。不同病毒组之间的核苷酸组成和密码子使用情况有所不同，例如正链RNA（+ssRNA）病毒的GC含量高于其他RNA病毒组。+ssRNA病毒的密码子使用情况更接近人类，其密码子适应指数（CAI）显著高于负链RNA（-ssRNA）病毒、双链RNA（dsRNA）病毒和逆转录病毒。双义病毒尽管GC含量较低，但其CAI与+ssRNA病毒相当，而dsRNA病毒的CAI最低。这可能对+ssRNA病毒有利，因为它们的基因组被用作mRNA。然而，对核苷酸组成对密码子使用影响的分析并未显示+ssRNA病毒和-ssRNA病毒之间存在差异。这表明基因组组成以及由此产生的突变压力仍然是导致不同基因组类型的RNA病毒密码子使用差异的主要压力。
