The codon usage pattern of the novel coronavirus

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.