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

• Tipo de documento: Artigo Científico
• Fonte: NPJ VACCINES; v. 9, n. 1, p. 12-pg., 2024-08-10.

Resumo

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)

• Processo FAPESP: 22/03645-1 - Estudo da interação vírus-vetor e dos mecanismos envolvidos na modulação da dinâmica de transmissão viral
• Beneficiário: Maurício Lacerda Nogueira
• Modalidade de apoio: Auxílio à Pesquisa - Temático
• Processo FAPESP: 20/10127-1 - Desenvolvimento de vacina contra a COVID-19
• Beneficiário: Dimas Tadeu Covas
• Modalidade de apoio: Auxílio à Pesquisa - Pesquisa em Políticas Públicas
• Processo FAPESP: 21/11944-6 - Contínuo aprimoramento de vacinas: Centro para Vigilância Viral e Avaliação Sorológica (CeVIVAS)
• Beneficiário: Sandra Coccuzzo Sampaio Vessoni
• Modalidade de apoio: Auxílio à Pesquisa - Centros de Ciência para o Desenvolvimento
• Processo FAPESP: 23/14670-0 - Análise do impacto da expressão de genes do sistema imune e da regulação por RNAs de interferência (RNAi) na resposta antiviral em insetos do gênero Aedes
• Beneficiário: Cecilia Artico Banho
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado
• Processo FAPESP: 20/04836-0 - Estudo clínico e epidemiológico de SARS-CoV-2 em uma coorte prospectiva populacional e hospitalar em São José do Rio Preto, São Paulo, Brasil, durante pandemia de 2020
• Beneficiário: Maurício Lacerda Nogueira
• Modalidade de apoio: Auxílio à Pesquisa - Regular