COVID-19 vaccination atlas using an integrative systems vaccinology approach

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

• Document type: Journal article
• Source: NPJ VACCINES; v. 10, n. 1, p. 12-pg., 2025-06-02.

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. (AU)

• FAPESP's process: 18/18886-9 - Systemic and integrative analysis of the immune response to Zika and Dengue viral infections
• Grantee: Otávio Cabral Marques
• Support Opportunities: Research Grants - Young Investigators Grants
• FAPESP's process: 23/07806-2 - Integrative systems bioinformatics analysis of antiviral immune responses.
• Grantee: Igor Salerno Filgueiras
• Support Opportunities: Scholarships in Brazil - Technical Training Program - Technical Training
• FAPESP's process: 19/01255-9 - Bats: epidemiological surveillance, high-resolution phylodynamics, search and design of peptides of biotechnological interest in emergent and reemerging viruses
• Grantee: Ricardo Durães de Carvalho
• Support Opportunities: Research Grants - Young Investigators Grants
• FAPESP's process: 19/14526-0 - Development of vaccines against Streptococcus pyogenes and Chikungunya Virus based on virus like particles
• Grantee: Gustavo Cabral de Miranda
• Support Opportunities: Research Grants - Young Investigators Grants
• FAPESP's process: 21/03684-4 - Bats: epidemiological surveillance, high-resolution phylodynamics, search and design of peptides of biotechnological interest in emergent and reemerging viruses
• Grantee: Ricardo Durães de Carvalho
• Support Opportunities: Scholarships in Brazil - Young Researchers
• FAPESP's process: 20/16246-2 - Holistic characterization of T cell exhaustion in patients with Zika
• Grantee: Dennyson Leandro Mathias da Fonseca
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• FAPESP's process: 23/13356-0 - The analysis of neutrophil-activating autoantibodies: a thrombosis perspective
• Grantee: Dennyson Leandro Mathias da Fonseca
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate (Direct)
• FAPESP's process: 20/05146-7 - Development of vaccine anti-SARS-CoV-2 based on VLPs
• Grantee: Gustavo Cabral de Miranda
• Support Opportunities: Regular Research Grants