Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage

F. G. Naveca; I. Claro; M. Giovanetti; J. G. Jesus; J. Xavier; F. C. M. Iani; V. A. do Nascimento; V. C. de Souza; P. P. Silveira; J. Lourenço; M. Santillana; M. U. G. Kraemer; J. Quick; S. C. Hill; J. Thézé; R. D. O. Carvalho; V. Azevedo; F. C. S. Salles; M. R. T. Nunes; P. S. Lemos; D. S. Candido; G. C. Pereira; M. A. A. Oliveira; C. A. R. Meneses; R. M. Maito; C. R. S. B. Cunha; D. P. S. Campos; M. C. Castilho; T. C. S. Siqueira; T. M. Terra; C. F. C. de Albuquerque; L. N. da Cruz; A. L. Abreu; D. V. Martins; D. S. M. V. Simoes; R. S. Aguiar; S. L. B. Luz; N. Loman; O. G. Pybus; E. C. Sabino; O. Okumoto; L. C. J. Alcantara; N. R. Faria

doi:10.1101/492595

Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage

F. G. Naveca, I. Claro, M. Giovanetti, J. G. Jesus, J. Xavier, F. C. M. Iani, V. A. do Nascimento, V. C. de Souza, P. P. Silveira, J. Lourenço, M. Santillana, M. U. G. Kraemer, J. Quick, S. C. Hill, J. Thézé, R. D. O. Carvalho, V. Azevedo, F. C. S. Salles, M. R. T. Nunes, P. S. LemosD. S. Candido, G. C. Pereira, M. A. A. Oliveira, C. A. R. Meneses, R. M. Maito, C. R. S. B. Cunha, D. P. S. Campos, M. C. Castilho, T. C. S. Siqueira, T. M. Terra, C. F. C. de Albuquerque, L. N. da Cruz, A. L. Abreu, D. V. Martins, D. S. M. V. Simoes, R. S. Aguiar, S. L. B. Luz, N. Loman, O. G. Pybus, E. C. Sabino, O. Okumoto, L. C. J. Alcantara, N. R. Faria

Research output: Working paper › Preprint

Abstract

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.

Original language	English
Publisher	bioRxiv
Number of pages	41
DOIs	https://doi.org/10.1101/492595
Publication status	Published - 10 Dec 2018
Externally published	Yes

Keywords

Chikungunya
East-Central-South-African
Surveillance
Amazon region
MinION genome sequencing
Traditional epidemiology
Genomic epidemiology
Digital epidemiology
Phylodynamics

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1101/492595Licence: CC BY

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Naveca, F. G., Claro, I., Giovanetti, M., Jesus, J. G., Xavier, J., Iani, F. C. M., Nascimento, V. A. D., Souza, V. C. D., Silveira, P. P., Lourenço, J., Santillana, M., Kraemer, M. U. G., Quick, J., Hill, S. C., Thézé, J., Carvalho, R. D. O., Azevedo, V., Salles, F. C. S., Nunes, M. R. T., ... Faria, N. R. (2018). Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage. bioRxiv. https://doi.org/10.1101/492595

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title = "Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage",

abstract = "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{\textquoteright}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.",

keywords = "Chikungunya, East-Central-South-African, Surveillance, Amazon region, MinION genome sequencing, Traditional epidemiology, Genomic epidemiology, Digital epidemiology, Phylodynamics",

author = "Naveca, \{F. G.\} and I. Claro and M. Giovanetti and Jesus, \{J. G.\} and J. Xavier and Iani, \{F. C. M.\} and Nascimento, \{V. A. do\} and Souza, \{V. C. de\} and Silveira, \{P. P.\} and J. Louren{\c c}o and M. Santillana and Kraemer, \{M. U. G.\} and J. Quick and Hill, \{S. C.\} and J. Th{\'e}z{\'e} and Carvalho, \{R. D. O.\} and V. Azevedo and Salles, \{F. C. S.\} and Nunes, \{M. R. T.\} and Lemos, \{P. S.\} and Candido, \{D. S.\} and Pereira, \{G. C.\} and Oliveira, \{M. A. A.\} and Meneses, \{C. A. R.\} and Maito, \{R. M.\} and Cunha, \{C. R. S. B.\} and Campos, \{D. P. S.\} and Castilho, \{M. C.\} and Siqueira, \{T. C. S.\} and Terra, \{T. M.\} and Albuquerque, \{C. F. C. de\} and Cruz, \{L. N. da\} and Abreu, \{A. L.\} and Martins, \{D. V.\} and Simoes, \{D. S. M. V.\} and Aguiar, \{R. S.\} and Luz, \{S. L. B.\} and N. Loman and Pybus, \{O. G.\} and Sabino, \{E. C.\} and O. Okumoto and Alcantara, \{L. C. J.\} and Faria, \{N. R.\}",

year = "2018",

month = dec,

day = "10",

doi = "10.1101/492595",

language = "English",

publisher = "bioRxiv",

type = "WorkingPaper",

institution = "bioRxiv",

}

Naveca, FG, Claro, I, Giovanetti, M, Jesus, JG, Xavier, J, Iani, FCM, Nascimento, VAD, Souza, VCD, Silveira, PP, Lourenço, J, Santillana, M, Kraemer, MUG, Quick, J, Hill, SC, Thézé, J, Carvalho, RDO, Azevedo, V, Salles, FCS, Nunes, MRT, Lemos, PS, Candido, DS, Pereira, GC, Oliveira, MAA, Meneses, CAR, Maito, RM, Cunha, CRSB, Campos, DPS, Castilho, MC, Siqueira, TCS, Terra, TM, Albuquerque, CFCD, Cruz, LND, Abreu, AL, Martins, DV, Simoes, DSMV, Aguiar, RS, Luz, SLB, Loman, N, Pybus, OG, Sabino, EC, Okumoto, O, Alcantara, LCJ & Faria, NR 2018 'Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage' bioRxiv. https://doi.org/10.1101/492595

TY - UNPB

T1 - Chikungunya virus outbreak in the Amazon region

T2 - replacement of the Asian genotype by an ECSA lineage

AU - Naveca, F. G.

AU - Claro, I.

AU - Giovanetti, M.

AU - Jesus, J. G.

AU - Xavier, J.

AU - Iani, F. C. M.

AU - Nascimento, V. A. do

AU - Souza, V. C. de

AU - Silveira, P. P.

AU - Lourenço, J.

AU - Santillana, M.

AU - Kraemer, M. U. G.

AU - Quick, J.

AU - Hill, S. C.

AU - Thézé, J.

AU - Carvalho, R. D. O.

AU - Azevedo, V.

AU - Salles, F. C. S.

AU - Nunes, M. R. T.

AU - Lemos, P. S.

AU - Candido, D. S.

AU - Pereira, G. C.

AU - Oliveira, M. A. A.

AU - Meneses, C. A. R.

AU - Maito, R. M.

AU - Cunha, C. R. S. B.

AU - Campos, D. P. S.

AU - Castilho, M. C.

AU - Siqueira, T. C. S.

AU - Terra, T. M.

AU - Albuquerque, C. F. C. de

AU - Cruz, L. N. da

AU - Abreu, A. L.

AU - Martins, D. V.

AU - Simoes, D. S. M. V.

AU - Aguiar, R. S.

AU - Luz, S. L. B.

AU - Loman, N.

AU - Pybus, O. G.

AU - Sabino, E. C.

AU - Okumoto, O.

AU - Alcantara, L. C. J.

AU - Faria, N. R.

PY - 2018/12/10

Y1 - 2018/12/10

N2 - 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.

AB - 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.

KW - Chikungunya

KW - East-Central-South-African

KW - Surveillance

KW - Amazon region

KW - MinION genome sequencing

KW - Traditional epidemiology

KW - Genomic epidemiology

KW - Digital epidemiology

KW - Phylodynamics

U2 - 10.1101/492595

DO - 10.1101/492595

M3 - Preprint

BT - Chikungunya virus outbreak in the Amazon region

PB - bioRxiv

ER -

Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage

Abstract

Keywords

UN SDGs

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