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Banho CA, de Carvalho Marques B, Sacchetto L, Sepedro Lima AK, Pereira Parra MC, Jeronimo Lima AR, Ribeiro G, Jorge Martins A, dos Santos Barros CR, Carolina Elias M, Coccuzzo Sampaio S, Nanev Slavov S, Strazza Rodrigues E, Vieira Santos E, Tadeu Covas D, Kashima S, Augusto Brassaloti R, Petry B, Gaspar Clemente L, Lehmann Coutinho L, Akemi Assato P, da Silva da Costa FA, Souza-Neto JA, Maria Tommasini Grotto R, Daiana Poleti M, Cristina Chagas Lesbon J, Chicaroni Mattos E, Fukumasu H, Giovanetti M, Carlos Junior Alcantara L, Rahal P, Pessoa Araújo JF, Althouse BM, Vasilakis N, Lacerda Nogueira M. Dynamic clade transitions and the influence of vaccine rollout on the spatiotemporal circulation of SARS-CoV-2 variants in São Paulo, Brazil. Res Sq 2024:rs.3.rs-3788142. [PMID: 38343798 PMCID: PMC10854302 DOI: 10.21203/rs.3.rs-3788142/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
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.
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Affiliation(s)
- Cecília Artico Banho
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Beatriz de Carvalho Marques
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Lívia Sacchetto
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Ana Karoline Sepedro Lima
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Maisa Carla Pereira Parra
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Alex Ranieri Jeronimo Lima
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Gabriela Ribeiro
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Antonio Jorge Martins
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | | | - Maria Carolina Elias
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Sandra Coccuzzo Sampaio
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Svetoslav Nanev Slavov
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Evandra Strazza Rodrigues
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Elaine Vieira Santos
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Dimas Tadeu Covas
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Simone Kashima
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | - Bruna Petry
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Luan Gaspar Clemente
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Luiz Lehmann Coutinho
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Patricia Akemi Assato
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Felipe Allan da Silva da Costa
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Jayme A. Souza-Neto
- São Paulo State University (UNESP), School of Agricultural Sciences, Botucatu, Brazil
| | - Rejane Maria Tommasini Grotto
- São Paulo State University (UNESP), School of Agricultural Sciences, Botucatu, Brazil
- Molecular Biology Laboratory, Applied Biotechnology Laboratory, Clinical Hospital of the Botucatu Medical School, Brazil
| | - Mirele Daiana Poleti
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Jessika Cristina Chagas Lesbon
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Elisangela Chicaroni Mattos
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Marta Giovanetti
- Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil
- Climate Amplified Diseases And Epidemics (CLIMADE), Brazil, Americas
- Sciences and Technologies for Sustainable Development and One Health, Universita Campus Bio-Medico di Roma, Italy
| | - Luiz Carlos Junior Alcantara
- Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil
- Climate Amplified Diseases And Epidemics (CLIMADE), Brazil, Americas
| | - Paula Rahal
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista (Unesp), São José do Rio Preto, Brazil
| | - João Fernando Pessoa Araújo
- Instituto de Biotecnologia, Universidade Estadual Paulista (Unesp), Botucatu, Brazil
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, Brazil
| | - Benjamin M. Althouse
- Department of Biology, New Mexico State University, Las Cruces, NM
- Information School, University of Washington, Seattle, WA
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch; Galveston, Texas, United States of America
- Center for Vector-Borne and Zoonotic Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
- Department of Pathology, University of Texas Medical Branch; Galveston, Texas, United States of America
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