The current outbreak of a novel coronavirus (COVID-19) has caused thousands of deaths and has been declared to be a worldwide pandemic by the World Health Organization. There have been various disputes but the origin of COVID-19 is not clear. Here we analyzed the similarities of codon usage patterns between humans and pathogenic viruses, such as human immunodeficiency virus (HIV), highly pathogenic avian influenza (HPAI), SARS, MERS, and COVID-19. In HIVs, HPAIs, SARS, and MERS, codon usages are highly similar to that of humans; in contrast, the codon usage pattern of COVID-19 is drastically different from those of humans and other pathogenic viruses. Besides, coronaviruses have been evolving in two opposite directions: human-preferred codons are adopted to substitute less-preferred ones in SARS and MERS but are substituted by less-preferred ones in COVID-19. The unique codon usage pattern suggesting that COVID-19 was evolved in an intermediate host, in which its codon usage pattern becomes drastically different from that of bats or humans, and its pathogenicity is weakened compared with SARS ad MERS COVs. Finally, we appeal to international cooperation to eliminate the epidemic by cutting off the transmission routes among humans and to search for the origin and intermediate hosts of the novel coronavirus to prevent future animal-to-human transmission.