The codon usage pattern of the novel coronavirus

<b> </b>The current outbreak of a novel coronavirus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2) is spreading rapidly across the whole world. The World Health Organization has declared the coronavirus diseases (COVID-19) to be a global pandemic. COVID-19 is milder, less fatal than SARS and MERS, but SARS-CoV-2 poses more serious threats to public health, because it is highly contagious and has a high potential of causing severe-acute, life-threatening pneumonia. Here we analyzed the similarities of codon usages between humans and different viruses, including human immunodeficiency virus (HIV), highly pathogenic avian influenza (HPAI), and coronavirus (CoV). The codon usages of HPAIs are highly similar to that of humans. In contrast, the codon usage of HIVs and CoVs is less and the codon usage of SARS-CoV-2 is the least similar to that of humans among all viruses tested. Besides, human-preferred codons are adopted to substitute less-preferred ones in SARS-CoV; in SARS-CoV-2, however, human-preferred codons are replaced by less-preferred ones. The unique codon usage pattern suggests that SARS-CoV-2 was probably formed by evolving in an unusual intermediate host over a long period, in which its codon usage became drastically different from that of humans and those of other pathogenic viruses. Moreover, its pathogenicity is weakened compared with SARS-CoV, but it becomes more potent and may gain higher potentials in the future. Therefore, there is an urgent need to block the transmission routes among humans, search for the origin and intermediate hosts of the coronaviruses, and prevent any future outbreaks.<br>