The evolution of SARS-CoV-2 and the COVID-19 pandemic

Yuanfang Si; Weidong Wu; Xia Xue; Xiangdong Sun; Yaping Qin; Ya Li; Chunjing Qiu; Yingying Li; Ziran Zhuo; Yang Mi; Pengyuan Zheng

doi:10.7717/peerj.15990

The evolution of SARS-CoV-2 and the COVID-19 pandemic

PeerJ. 2023 Sep 7:11:e15990. doi: 10.7717/peerj.15990. eCollection 2023.

Authors

Yuanfang Si^#^{1

2

3}, Weidong Wu^#⁴, Xia Xue^{1

2

3}, Xiangdong Sun^{1

2

3}, Yaping Qin⁵, Ya Li^{1

2

3}, Chunjing Qiu^{1

2

3}, Yingying Li^{1

2

3}, Ziran Zhuo⁴, Yang Mi^{1

2

3}, Pengyuan Zheng^{1

2

3}

Affiliations

¹ Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
² Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
³ Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China.
⁴ BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China.
⁵ School of Basic Medical Sciences, Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China.

^# Contributed equally.

Abstract

Scientists have made great efforts to understand the evolution of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) to provide crucial information to public health experts on strategies to control this viral pathogen. The pandemic of the coronavirus disease that began in 2019, COVID-19, lasted nearly three years, and nearly all countries have set different epidemic prevention policies for this virus. The continuous evolution of SARS-CoV-2 alters its pathogenicity and infectivity in human hosts, thus the policy and treatments have been continually adjusted. Based on our previous study on the dynamics of binding ability prediction between the COVID-19 spike protein and human ACE2, the present study mined over 10 million sequences and epidemiological data of SARS-CoV-2 during 2020-2022 to understand the evolutionary path of SARS-CoV-2. We analyzed and predicted the mutation rates of the whole genome and main proteins of SARS-CoV-2 from different populations to understand the adaptive relationship between humans and COVID-19. Our study identified a correlation of the mutation rates from each protein of SARS-CoV-2 and various human populations. Overall, this analysis provides a scientific basis for developing data-driven strategies to confront human pathogens.

Keywords: Epidemiology; Evolution; Interactions; Populations; Viral Proteins.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19* / epidemiology
Humans
Mutation Rate
Pandemics
Physicians*
SARS-CoV-2 / genetics

Grants and funding

This work was supported by the Zhengzhou Major Collaborative Innovation Project (No. 18XTZX12003), the Key projects of discipline construction in Zhengzhou University (No. XKZDJC202001), and the National key Research and development program in China (No. 2020YFC2006100). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.