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

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.

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Publication Details

Journal
npj Vaccines
Published
2024-08-10
DOI
https://doi.org/10.1038/s41541-024-00933-w
Citations
5
Primary Topic
SARS-CoV-2 and COVID-19 Research
Type
article
Field-Weighted Citation Impact
1.95

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article

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

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SARS-CoV-2 and COVID-19 Research
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article

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

Jéssika Cristina Chagas Lesbon, Maria Carolina Elias, Ricardo Augusto Brassaloti, Paula Rahal, Luan Gaspar Clemente, Cecília Ártico Banho, Maisa Carla Pereira Parra, Rejane Maria Tommasini Grotto, Evandra Strazza Rodrigues, Jayme A. Souza‐Neto, João Pessoa Araújo, Cláudia Renata dos Santos Barros, Felipe Allan da Silva da Costa, Dimas Tadeu Covas, Lívia Sacchetto, Benjamin M. Althouse, E. C. Mattos, Simone Kashima, Svetoslav Nanev Slavov, Bruna Petry, Beatriz de Carvalho Marques, Gabriela Ribeiro, Fernando Rosado Spilki, Mirele Poleti, Heidge Fukumasu, Luíz Carlos Júnior Alcântara, Antonio Jorge Martins, Nikos Vasilakis, Marta Giovanetti, Maurício Lacerda Nogueira, Luiz Lehmann Coutinho, Ana Karoline Sepedro Lima, Alex Ranieri Jerônimo Lima, Patrícia Akemi Assato, Sandra Coccuzzo Sampaio, Elaine Vieira Santos
article en
5 citations

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.

npj VaccinesVol. 9(1)
New Mexico State University (US), Faculdade de Medicina de São José do Rio Preto (BR), Climate Central (US), Universidade Feevale (BR), Università Campus Bio-Medico (IT), Universidade de São Paulo (BR), Kansas State University (US), University of Washington (US), Instituto Butantan (BR), Medecell (Brazil) (BR), Clinics Hospital of Ribeirão Preto (BR), Genomic (Brazil) (BR), Fundação Oswaldo Cruz (BR), The University of Texas Medical Branch at Galveston (US), Universidade Estadual Paulista (Unesp) (BR)
Fundação de Amparo à Pesquisa do Estado de São Paulo, Ministério da Ciência, Tecnologia e Inovação, Conselho Nacional de Desenvolvimento Científico e Tecnológico, Financiadora de Estudos e Projetos, Fundação Butantan, Faculdade de Medicina de São José do Rio Preto, National Institutes of Health
Good health and well-being
Openalex Percentile: Top 14%
SARS-CoV-2 and COVID-19 Research
1.95
DOIOpen Access PDFOpenAlex
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