npj Vaccines (Aug 2024)
Dynamic clade transitions and the influence of vaccination on the spatiotemporal circulation of SARS-CoV-2 variants
- Cecília Artico Banho,
- Beatriz de Carvalho Marques,
- Lívia Sacchetto,
- Ana Karoline Sepedro Lima,
- Maisa Carla Pereira Parra,
- Alex Ranieri Jeronimo Lima,
- Gabriela Ribeiro,
- Antonio Jorge Martins,
- Claudia Renata dos Santos Barros,
- Maria Carolina Elias,
- Sandra Coccuzzo Sampaio,
- Svetoslav Nanev Slavov,
- Evandra Strazza Rodrigues,
- Elaine Vieira Santos,
- Dimas Tadeu Covas,
- Simone Kashima,
- Ricardo Augusto Brassaloti,
- Bruna Petry,
- Luan Gaspar Clemente,
- Luiz Lehmann Coutinho,
- Patricia Akemi Assato,
- Felipe Allan da Silva da Costa,
- Rejane Maria Tommasini Grotto,
- Mirele Daiana Poleti,
- Jessika Cristina Chagas Lesbon,
- Elisangela Chicaroni Mattos,
- Heidge Fukumasu,
- Marta Giovanetti,
- Luiz Carlos Junior Alcantara,
- Jayme A. Souza-Neto,
- Paula Rahal,
- João Pessoa Araújo,
- Fernando Rosado Spilki,
- Benjamin M. Althouse,
- Nikos Vasilakis,
- Maurício Lacerda Nogueira
Affiliations
- Cecília Artico Banho
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto
- Beatriz de Carvalho Marques
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto
- Lívia Sacchetto
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto
- Ana Karoline Sepedro Lima
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto
- Maisa Carla Pereira Parra
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto
- Alex Ranieri Jeronimo Lima
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute
- Gabriela Ribeiro
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute
- Antonio Jorge Martins
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute
- Claudia Renata dos Santos Barros
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute
- Maria Carolina Elias
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute
- Sandra Coccuzzo Sampaio
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute
- Svetoslav Nanev Slavov
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute
- Evandra Strazza Rodrigues
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto
- Elaine Vieira Santos
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto
- Dimas Tadeu Covas
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute
- Simone Kashima
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto
- Ricardo Augusto Brassaloti
- University of São Paulo, Centro de Genômica Funcional da ESALQ
- Bruna Petry
- University of São Paulo, Centro de Genômica Funcional da ESALQ
- Luan Gaspar Clemente
- University of São Paulo, Centro de Genômica Funcional da ESALQ
- Luiz Lehmann Coutinho
- University of São Paulo, Centro de Genômica Funcional da ESALQ
- Patricia Akemi Assato
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology
- Felipe Allan da Silva da Costa
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology
- Rejane Maria Tommasini Grotto
- São Paulo State University (UNESP), School of Agricultural Sciences
- Mirele Daiana Poleti
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo
- Jessika Cristina Chagas Lesbon
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo
- Elisangela Chicaroni Mattos
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo
- Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo
- Marta Giovanetti
- Oswaldo Cruz Foundation, FIOCRUZ
- Luiz Carlos Junior Alcantara
- Oswaldo Cruz Foundation, FIOCRUZ
- Jayme A. Souza-Neto
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas StateUniversity
- Paula Rahal
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista (Unesp)
- João Pessoa Araújo
- Instituto de Biotecnologia, Universidade Estadual Paulista (Unesp)
- Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale
- Benjamin M. Althouse
- Department of Biology, New Mexico State University
- Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch
- Maurício Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto
- DOI
- https://doi.org/10.1038/s41541-024-00933-w
- Journal volume & issue
-
Vol. 9,
no. 1
pp. 1 – 12
Abstract
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.
