Dataset Information

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

ABSTRACT: BACKGROUND: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.

SUBMITTER: Naveca FG

PROVIDER: S-EPMC6424459 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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

Naveca Felipe Gomes FG Claro Ingra I Giovanetti Marta M de Jesus Jaqueline Goes JG Xavier Joilson J Iani Felipe Campos de Melo FCM do Nascimento Valdinete Alves VA de Souza Victor Costa VC Silveira Paola Paz PP Lourenço José J Santillana Mauricio M Kraemer Moritz U G MUG Quick Josh J Hill Sarah C SC Thézé Julien J Carvalho Rodrigo Dias de Oliveira RDO Azevedo Vasco V Salles Flavia Cristina da Silva FCDS Nunes Márcio Roberto Teixeira MRT Lemos Poliana da Silva PDS Candido Darlan da Silva DDS Pereira Glauco de Carvalho GC Oliveira Marluce Aparecida Assunção MAA Meneses Cátia Alexandra Ribeiro CAR Maito Rodrigo Melo RM Cunha Claudeth Rocha Santa Brígida CRSB Campos Daniela Palha de Sousa DPS Castilho Marcia da Costa MDC Siqueira Thalita Caroline da Silva TCDS Terra Tiza Matos TM de Albuquerque Carlos F Campelo CFC da Cruz Laura Nogueira LN Abreu André Luis de AL Martins Divino Valerio DV Simoes Daniele Silva de Moraes Vanlume DSMV Aguiar Renato Santana de RS Luz Sérgio Luiz Bessa SLB Loman Nicholas N Pybus Oliver G OG Sabino Ester C EC Okumoto Osnei O Alcantara Luiz Carlos Junior LCJ Faria Nuno Rodrigues NR

PLoS neglected tropical diseases 20190307 3

<h4>Background</h4>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. Th ...[more]

PMID: 30845267

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Project description:Outbreaks of the emerging arbovirus chikungunya virus (CHIKV) affect millions of individuals in Asia, Africa, and Latin America. Vector competence can be changed dramatically by single amino acid exchanges located predominantly within the CHIKV E1 and E2 envelope proteins, which are associated with enhanced transmissibility by anthropophilic Aedes mosquitoes. Commonly used reference assays for molecular surveillance cover only a few adaptive mutations within the envelope domains and have not been validated for all CHIKV genotypes. The recognized landscape of CHIKV adaptive mutations is thus likely incomplete. We designed two nested reverse transcription-PCR (RT-PCR) assays that cover hot spots of viral adaptation to vectors within the E1 and E2 genomic domains. Primers were designed in conserved genomic regions to allow broad usability across CHIKV genotypes. The sensitivity of both assays was at least equivalent to E1- and E2-based reference assays and robust among CHIKV genotypes at 51.4 IU/reaction (E1, 95% confidence interval [CI], 39.8 to 78.9) and 4.0 IU/reaction (E2, 95% CI, 2.0 to 7.4). Upon analysis of the complete known CHIKV genomic diversity, up to 11 nucleotide mismatches with CHIKV variants occurred under oligonucleotide binding sites of reference assays, potentially limiting assay sensitivity, whereas no critical mismatches occurred in the new assays. Specificity testing with nine alphaviruses representing all serocomplexes showed amplification of Mayaro virus and O'nyong-nyong virus by the E1-based assay, but not by the E2-based assay. The high sensitivity and specificity of the new E2-based assay may allow its diagnostic usage in resource-limited settings. The combined new assays allow improved molecular epidemiological surveillance of CHIKV globally.IMPORTANCE The life cycle of arboviruses relies on efficient infection of and transmission by arthropod vectors. Adaptation to new vectors can thus dramatically increase the geographic range of an arbovirus. Several adaptive mutations enhance chikungunya virus (CHIKV) transmissibility by different mosquito species. The appearance of those adaptive mutations has led to large-scale CHIKV outbreaks in Asia, Africa, and Europe. Molecular surveillance of circulating CHIKV strains for adaptive mutations contributes to precise risk assessments and efficient vector control and provides new insight into the evolution of vector adaptation. Existing assays for molecular CHIKV surveillance are limited by poor coverage of known adaptive mutations, low sensitivity, and cost-intensive deep sequencing approaches, preventing universal application. We developed two highly sensitive nested RT-PCR assays that cover hot spots of vector adaptation in CHIKV envelope domains. The new assays allow unprecedented molecular surveillance across all CHIKV genotypes and diagnostic use in resource-limited settings globally.

Dataset Information

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

Publications

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

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