COVID-19 vaccination atlas using an integrative systems vaccinology approach

Wasim Aluísio Prates-Syed; Dennyson Leandro Mathias da Fonseca; Shahab Zaki Pour; Aline Lira; Nelson Cortes; Jaqueline Dinis Queiroz Silva; Evelyn Carvalho; Igor Salerno Filgueiras; Tania Geraldine Churascari Vinces; Lena F Schimke; Lorena C S Chaves; Gerhard Wunderlich; Ricardo Durães-Carvalho; Haroldo Dutra Dias; Hans D Ochs; Niels O S Câmara; Helder I Nakaya; José E Krieger; Otavio Cabral-Marques; Gustavo Cabral-Miranda

doi:10.1038/s41541-025-01148-3

COVID-19 vaccination atlas using an integrative systems vaccinology approach

NPJ Vaccines. 2025 Jun 2;10(1):111. doi: 10.1038/s41541-025-01148-3.

Authors

Wasim Aluísio Prates-Syed^{1

2}, Dennyson Leandro Mathias da Fonseca^{2

3}, Shahab Zaki Pour⁴, Aline Lira^{1

2}, Nelson Cortes^{1

2}, Jaqueline Dinis Queiroz Silva^{1

5}, Evelyn Carvalho^{1

5}, Igor Salerno Filgueiras², Tania Geraldine Churascari Vinces⁶, Lena F Schimke^{2

7}, Lorena C S Chaves⁸, Gerhard Wunderlich⁶, Ricardo Durães-Carvalho⁹, Haroldo Dutra Dias^{7

10}, Hans D Ochs¹¹, Niels O S Câmara², Helder I Nakaya^{5

12}, José E Krieger¹³, Otavio Cabral-Marques^#^{2

7

14}, Gustavo Cabral-Miranda^#^{15

16}

Affiliations

¹ Institute of Tropical Medicine, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil.
² Institute of Biomedical Sciences (ICB), University of São Paulo (USP), São Paulo, Brazil.
³ Institute of Mathematics and Statistics (IME), University of Sao Paulo (USP), Sao Paulo, Brazil.
⁴ Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil.
⁵ Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.
⁶ Department of Parasitology, Institute of Biomedical Sciences (ICB), University of São Paulo (USP), São Paulo, Brazil.
⁷ Department of Medicine, Division of Molecular Medicine, Laboratory of Medical Investigation 29, University of São Paulo School of Medicine, São Paulo, Brazil.
⁸ Department of Biomedical Engineering, School of Medicine, Emory University, Atlanta, Georgia, USA.
⁹ São Paulo School of Medicine, Department of Microbiology, Immunology and Parasitology, and Department of Morphology and Genetics, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil.
¹⁰ Department of Neuroscience, Institute of Biomedical Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil.
¹¹ Department of Pediatrics, University of Washington School of Medicine, and Seattle Children's Research Institute, Seattle, WA, USA.
¹² Hospital Israelita Albert Einstein, São Paulo, Brazil.
¹³ Laboratory of Genetics and Molecular Cardiology, Heart Institute, Clinical Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil.
¹⁴ DO'R Institute for research, São Paulo, Brazil.
¹⁵ Institute of Tropical Medicine, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil. gcabral.miranda@usp.br.
¹⁶ Institute of Biomedical Sciences (ICB), University of São Paulo (USP), São Paulo, Brazil. gcabral.miranda@usp.br.

^# Contributed equally.

Abstract

The COVID-19 vaccinations have played a significant role in controlling the pandemic. To elucidate their impact on the immune system, a COVID-19 vaccination atlas was developed using an integrative systems vaccinology approach. The atlas includes 562 samples from 245 participants, including both healthy individuals and those infected with or without prior vaccination, and covers the administration of five vaccines in different regimens. Key findings include the identification of distinct immune markers that differentiate between vaccine types and infection statuses. We observed that mRNA vaccines induced transient but strong immune responses after booster doses, whereas viral vector vaccines showed sustained immune activation with infection, partially resembling the immune profile exhibited during infection. Heterologous vaccination regimens demonstrated enhanced immune diversification compared to homologous regimens. Finally, we described the immunological landscape of COVID-19 vaccines and vaccines against other pathogens, at the gene-level and in cell population dynamics.