Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023

Ministério da Saúde (MS), Departamento de Ciência e Tecnologia (DECIT). General Laboratories Coordination of Brazilian Ministry of Health (CGLab/MoH). UK Health Security Agency (UKHSA). Japan International Cooperation Agency (JICA). Coordination of Health Surveillance and Reference Laboratories of O...

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Autores: Arantes, Ighor, Gomes, Marcelo, Ito, Kimihito, Sarafim, Sharbilla, Gräf, Tiago, Miyajima, Fabio, Khouri, Ricardo, Carvalho, Felipe Cotrim de, Almeida, Walquiria Aparecida Ferreira de, Siqueira, Marilda Mendonça, Resende, Paola Cristina, Naveca, Felipe Gomes, Bello, Gonzalo
Tipo de documento: artigo
Estado:Versão publicada
Data de publicação:2024
País:Brasil
Recursos:Fundação Oswaldo Cruz (FIOCRUZ)
Repositório:Repositório Institucional da FIOCRUZ (ARCA)
Idioma:inglês
OAI Identifier:oai:arca.fiocruz.br:icict/64378
Acesso em linha:https://arca.fiocruz.br/handle/icict/64378
Access Level:Acceso aberto
Palavra-chave:SARS-CoV-2
Brasil
XBB
Filogeografia
SARI
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dc.title.none.fl_str_mv Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023
title Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023
spellingShingle Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023
Arantes, Ighor
SARS-CoV-2
Brasil
XBB
Filogeografia
SARI
SARS-CoV-2
Brasil
Filogeografia
title_short Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023
title_full Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023
title_fullStr Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023
title_full_unstemmed Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023
title_sort Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023
dc.creator.none.fl_str_mv Arantes, Ighor
Gomes, Marcelo
Ito, Kimihito
Sarafim, Sharbilla
Gräf, Tiago
Miyajima, Fabio
Khouri, Ricardo
Carvalho, Felipe Cotrim de
Almeida, Walquiria Aparecida Ferreira de
Siqueira, Marilda Mendonça
Resende, Paola Cristina
Naveca, Felipe Gomes
Bello, Gonzalo
author Arantes, Ighor
author_facet Arantes, Ighor
Gomes, Marcelo
Ito, Kimihito
Sarafim, Sharbilla
Gräf, Tiago
Miyajima, Fabio
Khouri, Ricardo
Carvalho, Felipe Cotrim de
Almeida, Walquiria Aparecida Ferreira de
Siqueira, Marilda Mendonça
Resende, Paola Cristina
Naveca, Felipe Gomes
Bello, Gonzalo
author_role author
author2 Gomes, Marcelo
Ito, Kimihito
Sarafim, Sharbilla
Gräf, Tiago
Miyajima, Fabio
Khouri, Ricardo
Carvalho, Felipe Cotrim de
Almeida, Walquiria Aparecida Ferreira de
Siqueira, Marilda Mendonça
Resende, Paola Cristina
Naveca, Felipe Gomes
Bello, Gonzalo
author2_role author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.other.none.fl_str_mv SARS-CoV-2
Brasil
XBB
Filogeografia
SARI
topic SARS-CoV-2
Brasil
XBB
Filogeografia
SARI
SARS-CoV-2
Brasil
Filogeografia
dc.subject.decs.none.fl_str_mv SARS-CoV-2
Brasil
Filogeografia
description Ministério da Saúde (MS), Departamento de Ciência e Tecnologia (DECIT). General Laboratories Coordination of Brazilian Ministry of Health (CGLab/MoH). UK Health Security Agency (UKHSA). Japan International Cooperation Agency (JICA). Coordination of Health Surveillance and Reference Laboratories of Oswaldo Cruz Foundation (CVSLR/FIOCRUZ). Centers for Disease Control and Prevention (CDC). Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq). INOVA Fiocruz. Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ). Fundação de Amparo a Pesquisa do Estado do Amazonas (FAPEAM). Agency for International Development (USAID). Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES).
publishDate 2024
dc.date.accessioned.fl_str_mv 2024-06-07T15:16:51Z
dc.date.available.fl_str_mv 2024-06-07T15:16:51Z
dc.date.issued.fl_str_mv 2024
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv ARANTES, Ighor et al. Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023. Microbiology Spectrum, v. 12, n. 3, p. 1-18, Mar. 2024.
dc.identifier.uri.fl_str_mv https://arca.fiocruz.br/handle/icict/64378
dc.identifier.issn.none.fl_str_mv 2165-0497
dc.identifier.doi.none.fl_str_mv 10.1128/spectrum.03831-23
identifier_str_mv ARANTES, Ighor et al. Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023. Microbiology Spectrum, v. 12, n. 3, p. 1-18, Mar. 2024.
2165-0497
10.1128/spectrum.03831-23
url https://arca.fiocruz.br/handle/icict/64378
dc.language.iso.fl_str_mv eng
language eng
dc.relation.isversionof.none.fl_str_mv https://www.arca.fiocruz.br/handle/icict/63811
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv American Society for Microbiology
publisher.none.fl_str_mv American Society for Microbiology
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
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spelling 2024-06-07T15:16:51Z2024-06-07T15:16:51Z2024ARANTES, Ighor et al. Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023. Microbiology Spectrum, v. 12, n. 3, p. 1-18, Mar. 2024.2165-0497https://arca.fiocruz.br/handle/icict/6437810.1128/spectrum.03831-23Ministério da Saúde (MS), Departamento de Ciência e Tecnologia (DECIT). General Laboratories Coordination of Brazilian Ministry of Health (CGLab/MoH). UK Health Security Agency (UKHSA). Japan International Cooperation Agency (JICA). Coordination of Health Surveillance and Reference Laboratories of Oswaldo Cruz Foundation (CVSLR/FIOCRUZ). Centers for Disease Control and Prevention (CDC). Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq). INOVA Fiocruz. Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ). Fundação de Amparo a Pesquisa do Estado do Amazonas (FAPEAM). Agency for International Development (USAID). Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES).Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Arbovírus e Vírus Hemorrágicos. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Grupo de Métodos Analíticos em Vigilância Epidemiológica. Rio de Janeiro, RJ, Brasil.International Institute for Zoonosis Control. Hokkaido University. Hokkaido, Japan.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Arbovírus e Vírus Hemorrágicos. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Virologia Molecular. Curitiba, PR, Brasil.Fundação Oswaldo Cruz. Fiocruz Ceará. Fortaleza, CE, Brasil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, Brasil.Secretaria de Vigilância em Saúde e Ambiente. Coordenação-Geral de Vigilância das Doenças Imunopreveníveis. Departamento do Programa Nacional de Imunizações. Brasília, DF, Brasil.Secretaria de Vigilância em Saúde e Ambiente. Coordenação-Geral de Vigilância das Doenças Imunopreveníveis. Departamento do Programa Nacional de Imunizações. Brasília, DF, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Arbovírus e Vírus Hemorrágicos. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Instituto Leônidas e Maria Deane. Núcleo de Vigilância de Vírus Emergentes, Reemergentes ou Negligenciados, Laboratório de Ecologia de Doenças Transmissíveis na Amazônia. Manaus, AM, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Arbovírus e Vírus Hemorrágicos. Rio de Janeiro, RJ, Brasil.The SARS-CoV-2 XBB is a group of highly immune-evasive lineages of the Omicron variant of concern that emerged by recombining BA.2-descendent lineages and spread worldwide during 2023. In this study, we combine SARS-CoV-2 genomic data (n = 11,065 sequences) with epidemiological data of severe acute respiratory infection (SARI) cases collected in Brazil between October 2022 and July 2023 to reconstruct the space-time dynamics and epidemiologic impact of XBB dissemination in the country. Our analyses revealed that the introduction and local emergence of lineages carrying convergent mutations within the Spike protein, especially F486P, F456L, and L455F, propelled the spread of XBB* lineages in Brazil. The average relative instantaneous reproduction numbers of XBB* + F486P, XBB* + F486P + F456L, and XBB* + F486P + F456L + L455F lineages in Brazil were estimated to be 1.24, 1.33, and 1.48 higher than that of other co-circulating lineages (mainly BQ.1*/BE*), respectively. Despite such a growth advantage, the dissemination of these XBB* lineages had a reduced impact on Brazil's epidemiological scenario concerning previous Omicron subvariants. The peak number of SARI cases from SARS-CoV-2 during the XBB wave was approximately 90%, 80%, and 70% lower than that observed during the previous BA.1*, BA.5*, and BQ.1* waves, respectively. These findings revealed the emergence of multiple XBB lineages with progressively increasing growth advantage, yet with relatively limited epidemiological impact in Brazil throughout 2023. The XBB* + F486P + F456L + L455F lineages stand out for their heightened transmissibility, warranting close monitoring in the months ahead. Importance: Brazil was one the most affected countries by the SARS-CoV-2 pandemic, with more than 700,000 deaths by mid-2023. This study reconstructs the dissemination of the virus in the country in the first half of 2023, a period characterized by the dissemination of descendants of XBB.1, a recombinant of Omicron BA.2 lineages evolved in late 2022. The analysis supports that XBB dissemination was marked by the continuous emergence of indigenous lineages bearing similar mutations in key sites of their Spike protein, a process followed by continuous increments in transmissibility, and without repercussions in the incidence of severe cases. Thus, the results suggest that the epidemiological impact of the spread of a SARS-CoV-2 variant is influenced by an intricate interplay of factors that extend beyond the virus's transmissibility alone. The study also underlines the need for SARS-CoV-2 genomic surveillance that allows the monitoring of its ever-shifting composition.engAmerican Society for Microbiologyhttps://www.arca.fiocruz.br/handle/icict/63811SARS-CoV-2BrasilXBBFilogeografiaSARISARS-CoV-2BrasilFilogeografiaSpatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZArantes, IghorGomes, MarceloIto, KimihitoSarafim, SharbillaGräf, TiagoMiyajima, FabioKhouri, RicardoCarvalho, Felipe Cotrim deAlmeida, Walquiria Aparecida Ferreira deSiqueira, Marilda MendonçaResende, Paola CristinaNaveca, Felipe GomesBello, GonzaloLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://arca.fiocruz.br/bitstreams/742f8136-0367-45f4-83a7-006e68ecfe59/download5a560609d32a3863062d77ff32785d58MD51falseAnonymousREADORIGINALArantes, Ighor et al. 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