Dynamic clade transitions and the influence of vaccination on the spatiotemporal circulation of SARS-CoV-2 variants

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Banho, Cecilia Artico ; Marques, Beatriz de Carvalho ; Sacchetto, Livia ; Lima, Ana Karoline Sepedro ; Parra, Maisa Carla Pereira ; Lima, Alex Ranieri Jeronimo ; Ribeiro, Gabriela ; Martins, Antonio Jorge ; Barros, Claudia Renata dos Santos ; Elias, Maria Carolina ; Sampaio, Sandra Coccuzzo ; Slavov, Svetoslav Nanev ; Rodrigues, Evandra Strazza ; Santos, Elaine Vieira ; Covas, Dimas Tadeu ; Kashima, Simone ; Brassaloti, Ricardo Augusto ; Petry, Bruna ; Clemente, Luan Gaspar ; Coutinho, Luiz Lehmann ; Assato, Patricia Akemi ; da Costa, Felipe Allan da Silva ; Grotto, Rejane Maria Tommasini ; Poleti, Mirele Daiana ; Lesbon, Jessika Cristina Chagas ; Mattos, Elisangela Chicaroni ; Fukumasu, Heidge ; Giovanetti, Marta ; Alcantara, Luiz Carlos Junior ; Souza-Neto, Jayme A. ; Rahal, Paula ; Araujo Jr, Joao Pessoa ; Spilki, Fernando Rosado ; Althouse, Benjamin M. ; Vasilakis, Nikos ; Nogueira, Mauricio Lacerda

• Document type: Journal article
• Source: NPJ VACCINES; v. 9, n. 1, p. 12-pg., 2024-08-10.

Abstract

Since 2021, the emergence of variants of concern (VOC) has led Brazil to experience record numbers of in COVID-19 cases and deaths. The expanded spread of the SARS-CoV-2 combined with a low vaccination rate has contributed to the emergence of new mutations that may enhance viral fitness, leading to the persistence of the disease. Due to limitations in the real-time genomic monitoring of new variants in some Brazilian states, we aimed to investigate whether genomic surveillance, coupled with epidemiological data and SARS-CoV-2 variants spatiotemporal spread in a smaller region, can reflect the pandemic progression at a national level. Our findings revealed three SARS-CoV-2 variant replacements from 2021 to early 2022, corresponding to the introduction and increase in the frequency of Gamma, Delta, and Omicron variants, as indicated by peaks of the Effective Reproductive Number (Reff). These distinct clade replacements triggered two waves of COVID-19 cases, influenced by the increasing vaccine uptake over time. Our results indicated that the effectiveness of vaccination in preventing new cases during the Delta and Omicron circulations was six and eleven times higher, respectively, than during the period when Gamma was predominant, and it was highly efficient in reducing the number of deaths. Furthermore, we demonstrated that genomic monitoring at a local level can reflect the national trends in the spread and evolution of SARS-CoV-2. (AU)

• FAPESP's process: 22/03645-1 - Study of the virus-vector interaction and the mechanisms involved in modulating the dynamics of viral transmission
• Grantee: Maurício Lacerda Nogueira
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 20/10127-1 - Development of vaccine against COVID-19
• Grantee: Dimas Tadeu Covas
• Support Opportunities: Research Grants - Research in Public Policies
• FAPESP's process: 21/11944-6 - Continuous improvement of vaccines: Center for Viral Surveillance and Serological Assessment (CeVIVAS)
• Grantee: Sandra Coccuzzo Sampaio Vessoni
• Support Opportunities: Research Grants - Science Centers for Development
• FAPESP's process: 23/14670-0 - Impact of the immune genes expression and the regulation mechanisms modulated by small-interfering RNAs in the antiviral response of Aedes mosquitoes.
• Grantee: Cecilia Artico Banho
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 20/04836-0 - Clinical and epidemiological study of SARS-CoV-2 in a prospective population and hospitalar cohorts in São José do Rio Preto, SP, Brazil in 2020
• Grantee: Maurício Lacerda Nogueira
• Support Opportunities: Regular Research Grants