  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative
agent of the current global COVID-19 pandemic, in which millions of lives have
been lost. Understanding the zoonotic evolution of the coronavirus may provide
insights for developing effective vaccines, monitoring the transmission trends,
and preventing new zoonotic infections. Homopolymeric nucleotide repeats (HP),
the most simple tandem repeats, are a ubiquitous feature of eukaryotic genomes.
Yet the HP distributions and roles in coronavirus genome evolution are poorly
investigated. In this study, we characterize the HP distributions and trends in
the genomes of bat and human coronaviruses and SARS-CoV-2 variants. The results
show that the SARS-CoV-2 genome is abundant in HPs, and has augmented HP
contents during evolution. Especially, the disparity of HP poly-(A/T) and
ploy-(C/G) of coronaviruses increases during the evolution in human hosts. The
disparity of HP poly-(A/T) and ploy-(C/G) is correlated to host adaptation and
the virulence level of the coronaviruses. Therefore, we propose that the HP
disparity can be a quantitative measure for the zoonotic evolution levels of
coronaviruses. Peculiarly, the HP disparity measure infers that SARS-CoV-2
Omicron variants have a high disparity of HP poly-(A/T) and ploy-(C/G),
suggesting a high adaption to the human hosts.
