Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon

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dc.creatorFelipe Gomes Naveca
dc.creatorJosé Lourenço
dc.creatorMauricio Santillana
dc.creatorMoritz U. G. Kraemer
dc.creatorJosh Quick
dc.creatorSarah C. Hill
dc.creator‪Julien Thézé‬
dc.creatorRodrigo Dias de Oliveira Carvalho
dc.creatorVasco Ariston de Carvalho Azevedo
dc.creatorFlavia Cristina da Silva Salles
dc.creatorMárcio Roberto Teixeira Nunes
dc.creatorIngra Claro
dc.creatorPoliana da Silva Lemos
dc.creatorDarlan da Silva Candido
dc.creatorGlauco de Carvalho Pereira
dc.creatorMarluce Aparecida Assunção Oliveira
dc.creatorCátia Alexandra Ribeiro Meneses
dc.creatorRodrigo Melo Maito
dc.creatorClaudeth Rocha Santa Brígida Cunha
dc.creatorDaniela Palha de Sousa Campos
dc.creatorMarcia da Costa Castilho
dc.creatorThalita Caroline da Silva Siqueira
dc.creatorMarta Giovanetti
dc.creatorTiza Matos Terra
dc.creatorCarlos Campelo de Albuquerque
dc.creatorLaura Nogueira da Cruz
dc.creatorAndré Luis de Abreu
dc.creatorDivino Valerio Martins
dc.creatorDaniele Silva de Moraes Vanlume Simoes
dc.creatorRenato Santana de Aguiar
dc.creatorSérgio Luiz Bessa Luz
dc.creatorNicholas Loman
dc.creatorOliver G. Pybus
dc.creatorJaqueline Goes de Jesus
dc.creatorEster C. Sabino
dc.creatorOsnei Okumoto
dc.creatorLuiz Carlos Junior Alcantara
dc.creatorNuno Rodrigues Faria
dc.creatorJoilson Xavier
dc.creatorFelipe Campos de Melo Iani
dc.creatorValdinete Alves do Nascimento
dc.creatorVictor Costa de Souza
dc.creatorPaola Paz Silveira
dc.date.accessioned2023-07-17T18:04:21Z
dc.date.accessioned2025-09-09T01:03:54Z
dc.date.available2023-07-17T18:04:21Z
dc.date.issued2019
dc.identifier.doihttps://doi.org/10.1371/journal.pntd.0007065
dc.identifier.issn1935-2735
dc.identifier.urihttps://hdl.handle.net/1843/56419
dc.languagepor
dc.publisherUniversidade Federal de Minas Gerais
dc.relation.ispartofPLOS Neglected Tropical Diseases
dc.rightsAcesso Aberto
dc.subjectAmazônia
dc.subjectChikungunya
dc.subjectGenômica
dc.subject.otherBrazilian Amazon
dc.subject.otherChikungunya virus
dc.subject.otherGenomic
dc.titleGenomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon
dc.typeArtigo de periódico
local.citation.epage21
local.citation.issue3
local.citation.spage1
local.citation.volume13
local.description.resumoBackground Since its first detection in the Caribbean in late 2013, chikungunya virus (CHIKV) has affected 51 countries in the Americas. The CHIKV epidemic in the Americas was caused by the CHIKV-Asian genotype. In August 2014, local transmission of the CHIKV-Asian genotype was detected in the Brazilian Amazon region. However, a distinct lineage, the CHIKV-East-Central-South-America (ECSA)-genotype, was detected nearly simultaneously in Feira de Santana, Bahia state, northeast Brazil. The genomic diversity and the dynamics of CHIKV in the Brazilian Amazon region remains poorly understood despite its importance to better understand the epidemiological spread and public health impact of CHIKV in the country. Methodology/Principal findings We report a large CHIKV outbreak (5,928 notified cases between August 2014 and August 2018) in Boa vista municipality, capital city of Roraima’s state, located in the Brazilian Amazon region. We generated 20 novel CHIKV-ECSA genomes from the Brazilian Amazon region using MinION portable genome sequencing. Phylogenetic analyses revealed that despite an early introduction of the Asian genotype in 2015 in Roraima, the large CHIKV outbreak in 2017 in Boa Vista was caused by an ECSA-lineage most likely introduced from northeastern Brazil. Epidemiological analyses suggest a basic reproductive number of R0 of 1.66, which translates in an estimated 39 (95% CI: 36 to 45) % of Roraima’s population infected with CHIKV-ECSA. Finally, we find a strong association between Google search activity and the local laboratory-confirmed CHIKV cases in Roraima. Conclusions/Significance This study highlights the potential of combining traditional surveillance with portable genome sequencing technologies and digital epidemiology to inform public health surveillance in the Amazon region. Our data reveal a large CHIKV-ECSA outbreak in Boa Vista, limited potential for future CHIKV outbreaks, and indicate a replacement of the Asian genotype by the ECSA genotype in the Amazon region. Author summary Until the end of 2017, Brazil notified the highest number of infections caused by chikungunya virus (CHIKV) in the Americas. We investigated a large CHIKV outbreak in Boa vista municipality in the Brazilian Amazon region. Rapid portable genome sequencing of 20 novel isolates and subsequent genetic analysis revealed that ECSA lineage was introduced from northeastern Brazil to Roraima around July 2016. Epidemiological analyses suggest a basic reproductive number of R0 of 1.66, which suggests that approximately 39% of Roraima’s population was infected with CHIKV-ECSA. Given the dominance of the CHIKV-Asian genotype in the Americas, our data highlights the rapid spread of a less understood and poorly characterized CHIKV-ECSA genotype in Brazil. Investigations on potential associations between public health impact of CHIKV and genetic diversity of circulating strains are warranted to better evaluate its impact in Brazil and beyond.
local.identifier.orcidhttps://orcid.org/0000-0002-2888-1060
local.identifier.orcidhttp://orcid.org/0000-0002-9318-2581
local.identifier.orcidhttps://orcid.org/0000-0002-4206-418X
local.identifier.orcidhttps://orcid.org/0000-0001-8637-2910
local.identifier.orcidhttps://orcid.org/0000-0003-1271-8549
local.identifier.orcidhttps://orcid.org/0000-0002-5080-3130
local.identifier.orcidhttps://orcid.org/0000-0003-1651-7066
local.identifier.orcidhttps://orcid.org/0000-0002-6344-2143
local.identifier.orcidhttps://orcid.org/0009-0007-9624-6222
local.identifier.orcidhttps://orcid.org/0009-0009-0769-3827
local.identifier.orcidhttps://orcid.org/0000-0001-7411-7445
local.identifier.orcidhttps://orcid.org/0000-0003-2657-4400
local.identifier.orcidhttps://orcid.org/0000-0001-5180-3717
local.identifier.orcidhttps://orcid.org/0000-0001-5887-7372
local.identifier.orcidhttps://orcid.org/0000-0002-9843-8988
local.identifier.orcidhttps://orcid.org/0000-0002-8797-2667
local.identifier.orcidhttps://orcid.org/0000-0002-3629-8529
local.identifier.orcidhttps://orcid.org/0000-0002-7786-4718
local.identifier.orcidhttps://orcid.org/0000-0002-3669-2219
local.publisher.countryBrasil
local.publisher.departmentICB - INSTITUTO DE CIÊNCIAS BIOLOGICAS
local.publisher.initialsUFMG
local.url.externahttps://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0007065

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