Evolutionary dynamics of SARS-CoV-2 variants under strict non-pharmaceutical interventions – a population-based study

Authors

  • Xiang Huo Army Medical University (Third Military Medical University), Chongqing, PRC https://orcid.org/0000-0002-5968-6874
  • Lunbiao Cui NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC https://orcid.org/0000-0001-6212-6053
  • Liguo Zhu NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC https://orcid.org/0000-0002-0636-4089
  • Jun Zhang Yangzhou Center for Disease Control and Prevention, Yangzhou, PRC
  • Huafeng Fan Nanjing Municipal Center for Disease Control and Prevention, Nanjing, PRC
  • Yongxiang Yi Nanjing Infectious Diseases Clinical Medical Center (The Second Hospital of Nanjing, Nanjing University of Chinese Medicine), Nanjing, PRC
  • Jun Zhao The Third People's Hospital of Yangzhou, Yangzhou, PRC
  • Yiyue Ge NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC
  • Shenjiao Wang NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC
  • Xu Han Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PRC
  • Xingsu Gao Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PRC
  • Xian Qi NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC
  • Jianguang Fu NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC
  • Zhifeng Li NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC
  • Huan Fan NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC
  • Huiyan Yu NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC
  • Fei Deng NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC
  • Kangchen Zhao NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC
  • Xiaojuan Zhu NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC
  • Jianli Hu NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC
  • Jianjun Li NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC https://orcid.org/0000-0003-4952-0077
  • Jing Ai NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC
  • Guodong Kang NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC
  • Ya Shen NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC
  • Guangjie Jin NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC
  • Furu Wang NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC
  • Zhong Zhang Nanjing Municipal Center for Disease Control and Prevention, Nanjing, PRC
  • Min He Nanjing Municipal Center for Disease Control and Prevention, Nanjing, PRC
  • Songning Ding Nanjing Municipal Center for Disease Control and Prevention, Nanjing, PRC
  • Yin Wang Yangzhou Center for Disease Control and Prevention, Yangzhou, PRC
  • Yuying Dong Yangzhou Center for Disease Control and Prevention, Yangzhou, PRC
  • Yao Huang Yangzhou Center for Disease Control and Prevention, Yangzhou, PRC
  • Changhua Yi Nanjing Infectious Diseases Clinical Medical Center (The Second Hospital of Nanjing, Nanjing University of Chinese Medicine), Nanjing, PRC
  • Longyu Wang Nanjing Infectious Diseases Clinical Medical Center (The Second Hospital of Nanjing, Nanjing University of Chinese Medicine), Nanjing, PRC
  • Yudong Jiao The Third People's Hospital of Yangzhou, Yangzhou, PRC
  • Jinfu Wang The Third People's Hospital of Yangzhou, Yangzhou, PRC
  • Jian Li Southeast University, Nanjing, PRC
  • Hongde Liu Southeast University, Nanjing, PRC
  • Jingxin Li NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC
  • Changjun Bao NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC
  • Ming Wu NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, PRC
  • Fengcai Zhu Army Medical University (Third Military Medical University), Chongqing, PRC

DOI:

https://doi.org/10.3855/jidc.19409

Keywords:

SARS-CoV-2, single nucleotide variation, non-pharmaceutical intervention, zero-COVID

Abstract

Introduction: China implemented a dynamic zero-COVID strategy to curb viral transmission in response to the coronavirus disease 2019 (COVID-19) pandemic. This strategy was designed to inhibit mutation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19. This study explores the dynamics of viral evolution under stringent non-pharmaceutical interventions (NPIs) through real-world observations.

Methodology: Our analysis encompassed all polymerase chain reaction (PCR)-confirmed COVID-19 cases (n = 780) from two consecutive outbreaks occurring in July to August 2021. Epidemiological investigations and in-depth viral genome analyses were conducted to determine the sources of infection and the inter-outbreak linkages.

Results: The outbreaks likely originated via contaminated objects from an imported COVID-19 case to local airport cleaners. Most patients presented clinically mild symptoms. All viral genomes clustered into a single clade, with genomes from the subsequent Yangzhou outbreak forming a distinct branch, diverging from those of the initial Nanjing outbreak. Compared to the Wuhan-Hu-1 strain, the Delta variants isolated from the imported case and early local cases in Nanjing had 35 nucleotide mutations and three deletions. Various single nucleotide variant (SNV) combinations were observed in subsequent transmissions, with NPIs accounting for the termination of 67.2% (92/137) of SNV combinations. Stringent implementation of NPIs resulted in a greater number of terminated SNV combinations than emerging ones. Additionally, vaccination of cases was associated with SNV combination termination.

Conclusions: This study underscores the significant role of NPIs in preventing the accumulation of SARS-CoV-2 mutations.

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Published

2024-12-31

How to Cite

1.
Huo X, Cui L, Zhu L, Zhang J, Fan H, Yi Y, Zhao J, Ge Y, Wang S, Han X, Gao X, Qi X, Fu J, Li Z, Fan H, Yu H, Deng F, Zhao K, Zhu X, Hu J, Li J, Ai J, Kang G, Shen Y, Jin G, Wang F, Zhang Z, He M, Ding S, Wang Y, Dong Y, Huang Y, Yi C, Wang L, Jiao Y, Wang J, Li J, Liu H, Li J, Bao C, Wu M, Zhu F (2024) Evolutionary dynamics of SARS-CoV-2 variants under strict non-pharmaceutical interventions – a population-based study. J Infect Dev Ctries 18:S214-S226. doi: 10.3855/jidc.19409

Issue

Vol. 18 No. 12.1: December 2024 -- SUPPLEMENT

Section

Coronavirus Pandemic

License

Copyright (c) 2024 Xiang Huo, Lunbiao Cui, Liguo Zhu, Jun Zhang, Huafeng Fan, Yongxiang Yi, Jun Zhao, Yiyue Ge, Shenjiao Wang, Xu Han, Xingsu Gao, Xian Qi , Jianguang Fu, Zhifeng Li, Huan Fan, Huiyan Yu, Fei Deng, Kangchen Zhao, Xiaojuan Zhu, Jianli Hu, Jianjun Li, Jing Ai, Guodong Kang, Ya Shen, Guangjie Jin, Furu Wang, Zhong Zhang, Min He, Songning Ding, Yin Wang, Yuying Dong, Yao Huang, Changhua Yi, Longyu Wang, Yudong Jiao, Jinfu Wang, Jian Li, Hongde Liu, Jingxin Li, Changjun Bao, Ming Wu, Fengcai Zhu

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