Evolutionary trend of SARS-CoV-2 inferred by the homopolymeric nucleotide repeats

TL;DR

This study investigates the distribution and evolution of homopolymeric nucleotide repeats in coronavirus genomes, revealing their potential as markers for zoonotic adaptation and highlighting increased disparity in SARS-CoV-2 variants like Omicron.

Contribution

It introduces the analysis of homopolymeric nucleotide repeats as a novel measure for tracking coronavirus evolution and host adaptation, especially in SARS-CoV-2 variants.

Findings

SARS-CoV-2 genomes are rich in homopolymeric repeats.

HP content increases during coronavirus evolution.

High HP disparity correlates with host adaptation and virulence.

Abstract

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.