Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage
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 Brazi...
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ir-iec-36482019-08-19T19:37:30Z Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage Naveca, Felipe Gomes Claro, Ingra Giovanetti, Marta Jesus, Jaqueline Goes de Xavier, Joilson Iani, Felipe Campos de Melo Nascimento, Valdinete Alves do Souza, Victor Costa de Silveira, Paola Paz Louren?o, Jos? Santillana, Mauricio Kraemer, Moritz U. G Quick, Josh Hill, Sarah C Treze, Julien Carvalho, Rodrigo Dias de Oliveira Azevedo, Vasco Sales, Flavia Cristina da Silva Nunes, M?rcio Roberto Teixeira Lemos, Poliana da Silva Candido, Darlan da Silva Pereira, Glauco de Carvalho Oliveira, Marluce Aparecida Assun??o Meneses, Catia Alexandra Ribeiro Maito, Rodrigo Melo Cunha, Claudeth Rocha Santa Br?gida Campos, Daniela Palha de Sousa Castilho, Marcia da Costa Siqueira, Thalita Caroline da Silva Terra, Tiza Matos Albuquerque, Carlos F. Campelo de Cruz, Laura Nogueira da Abreu, Andr? Luis de Martins, Divino Valerio Simoes, Daniele Silva de Moraes Vanlume Aguiar, Renato Santana de Luz, Sergio Luiz Bessa Loman, Nicholas Pybus, Oliver G Sabino, Ester Cerdeira Okumoto, Osnei Alc?ntara, Luiz Carlos Junior Faria, Nuno Rodrigues Arbovirus / isolamento & purifica??o V?rus Chikungunya / patogenicidade Genoma Viral / gen?tica Filogenia Sequenciamento Completo do Genoma Feira de Santana (BA) Boa vista (RR) 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. In just 48 hours, 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. 2019-04-15T13:54:49Z 2019-04-15T13:54:49Z 2018 Artigo NAVECA, Felipe Gomes et al. Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage. bioRxiv, e492595, p. 1-41, 2018. http://patua.iec.gov.br//handle/iec/3648 10.1101/492595 eng Acesso Aberto application/pdf Cold Spring Harbor Laboratory |
| institution |
Instituto Evandro Chagas (IEC) |
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PATUA |
| language |
eng |
| topic |
Arbovirus / isolamento & purifica??o V?rus Chikungunya / patogenicidade Genoma Viral / gen?tica Filogenia Sequenciamento Completo do Genoma Feira de Santana (BA) Boa vista (RR) |
| spellingShingle |
Arbovirus / isolamento & purifica??o V?rus Chikungunya / patogenicidade Genoma Viral / gen?tica Filogenia Sequenciamento Completo do Genoma Feira de Santana (BA) Boa vista (RR) Naveca, Felipe Gomes Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage |
| topic_facet |
Arbovirus / isolamento & purifica??o V?rus Chikungunya / patogenicidade Genoma Viral / gen?tica Filogenia Sequenciamento Completo do Genoma Feira de Santana (BA) Boa vista (RR) |
| description |
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. In just 48 hours, 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. |
| format |
Artigo |
| author |
Naveca, Felipe Gomes |
| author2 |
Claro, Ingra Giovanetti, Marta Jesus, Jaqueline Goes de Xavier, Joilson Iani, Felipe Campos de Melo Nascimento, Valdinete Alves do Souza, Victor Costa de Silveira, Paola Paz Louren?o, Jos? Santillana, Mauricio Kraemer, Moritz U. G Quick, Josh Hill, Sarah C Treze, Julien Carvalho, Rodrigo Dias de Oliveira Azevedo, Vasco Sales, Flavia Cristina da Silva Nunes, M?rcio Roberto Teixeira Lemos, Poliana da Silva Candido, Darlan da Silva Pereira, Glauco de Carvalho Oliveira, Marluce Aparecida Assun??o Meneses, Catia Alexandra Ribeiro Maito, Rodrigo Melo Cunha, Claudeth Rocha Santa Br?gida Campos, Daniela Palha de Sousa Castilho, Marcia da Costa Siqueira, Thalita Caroline da Silva Terra, Tiza Matos Albuquerque, Carlos F. Campelo de Cruz, Laura Nogueira da Abreu, Andr? Luis de Martins, Divino Valerio Simoes, Daniele Silva de Moraes Vanlume Aguiar, Renato Santana de Luz, Sergio Luiz Bessa Loman, Nicholas Pybus, Oliver G Sabino, Ester Cerdeira Okumoto, Osnei Alc?ntara, Luiz Carlos Junior Faria, Nuno Rodrigues |
| author2Str |
Claro, Ingra Giovanetti, Marta Jesus, Jaqueline Goes de Xavier, Joilson Iani, Felipe Campos de Melo Nascimento, Valdinete Alves do Souza, Victor Costa de Silveira, Paola Paz Louren?o, Jos? Santillana, Mauricio Kraemer, Moritz U. G Quick, Josh Hill, Sarah C Treze, Julien Carvalho, Rodrigo Dias de Oliveira Azevedo, Vasco Sales, Flavia Cristina da Silva Nunes, M?rcio Roberto Teixeira Lemos, Poliana da Silva Candido, Darlan da Silva Pereira, Glauco de Carvalho Oliveira, Marluce Aparecida Assun??o Meneses, Catia Alexandra Ribeiro Maito, Rodrigo Melo Cunha, Claudeth Rocha Santa Br?gida Campos, Daniela Palha de Sousa Castilho, Marcia da Costa Siqueira, Thalita Caroline da Silva Terra, Tiza Matos Albuquerque, Carlos F. Campelo de Cruz, Laura Nogueira da Abreu, Andr? Luis de Martins, Divino Valerio Simoes, Daniele Silva de Moraes Vanlume Aguiar, Renato Santana de Luz, Sergio Luiz Bessa Loman, Nicholas Pybus, Oliver G Sabino, Ester Cerdeira Okumoto, Osnei Alc?ntara, Luiz Carlos Junior Faria, Nuno Rodrigues |
| title |
Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage |
| title_short |
Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage |
| title_full |
Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage |
| title_fullStr |
Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage |
| title_full_unstemmed |
Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage |
| title_sort |
chikungunya virus outbreak in the amazon region: replacement of the asian genotype by an ecsa lineage |
| publisher |
Cold Spring Harbor Laboratory |
| publishDate |
2019 |
| url |
http://patua.iec.gov.br//handle/iec/3648 |
| _version_ |
1717584423135739904 |
| score |
11.755432 |