1. Vaccination Shapes Within-Host SARS-CoV-2 Diversity of Omicron BA.2.2 Breakthrough Infection.
- Author
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Zhang Y, Zhou Y, Chen J, Wu J, Wang X, Zhang Y, Wang S, Cui P, Xu Y, Li Y, Shen Z, Xu T, Zhang Q, Cai J, Zhang H, Wang P, Ai J, Jiang N, Qiu C, and Zhang W
- Subjects
- Humans, China, Epitopes, T-Lymphocyte immunology, Epitopes, T-Lymphocyte genetics, Mutation, Amino Acid Substitution, Genetic Variation, Male, Female, Breakthrough Infections, SARS-CoV-2 immunology, SARS-CoV-2 genetics, COVID-19 immunology, COVID-19 prevention & control, COVID-19 virology, COVID-19 Vaccines immunology, COVID-19 Vaccines administration & dosage, Vaccination, Spike Glycoprotein, Coronavirus genetics, Spike Glycoprotein, Coronavirus immunology
- Abstract
Background: Low-frequency intrahost single-nucleotide variants of SARS-CoV-2 have been recognized as predictive indicators of selection. However, the impact of vaccination on the intrahost evolution of SARS-CoV-2 remains uncertain at present., Methods: We investigated the genetic variation of SARS-CoV-2 in individuals who were unvaccinated, partially vaccinated, or fully vaccinated during Shanghai's Omicron BA.2.2 wave. We substantiated the connection between particular amino acid substitutions and immune-mediated selection through a pseudovirus neutralization assay or by cross-verification with the human leukocyte antigen-associated T-cell epitopes., Results: In contrast to those with immunologic naivety or partial vaccination, participants who were fully vaccinated had intrahost variant spectra characterized by reduced diversity. Nevertheless, the distribution of mutations in the fully vaccinated group was enriched in the spike protein. The distribution of intrahost single-nucleotide variants in individuals who were immunocompetent did not demonstrate notable signs of positive selection, in contrast to the observed adaptation in 2 participants who were immunocompromised who had an extended period of viral shedding., Conclusions: In SARS-CoV-2 infections, vaccine-induced immunity was associated with decreased diversity of within-host variant spectra, with milder inflammatory pathophysiology. The enrichment of mutations in the spike protein gene indicates selection pressure exerted by vaccination on the evolution of SARS-CoV-2., Competing Interests: Potential conflicts of interest All authors: No reported conflicts. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest., (© The Author(s) 2023. Published by Oxford University Press on behalf of Infectious Diseases Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2024
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