TY - JOUR
T1 - Epidemiological and genomic investigation of chikungunya virus in Rio de Janeiro state, Brazil, between 2015 and 2018
AU - Rebello Moreira, Filipe Romero
AU - de Menezes, Mariane Talon
AU - Salgado-Benvindo, Clarisse
AU - Whittaker, Charles
AU - Cox, Victoria
AU - Chandradeva, Nilani
AU - Souza de Paula, Hury Hellen
AU - Martins, Andréfrederico
AU - Das Chagas, Raphael Rangel
AU - Vargas Brasil, Rodrigo Decembrino
AU - Silva Cândido, Darlan da
AU - Herlinger, Alice Laschuk
AU - Ribeiro, Marisa de Oliveira
AU - Arruda, Monica Barcellos
AU - Alvarez, Patricia
AU - de Paula Tôrres, Marcelo Calado
AU - Dorigatti, Ilaria
AU - Brady, Oliver
AU - Moreira Voloch, Carolina
AU - Tanuri, Amilcar
AU - Iani, Felipe
AU - Souza, William Marciel de
AU - Cardozo, Sergian Vianna
AU - Faria, Nuno Rodrigues
AU - Aguiar, Renato Santana
N1 - Publisher Copyright:
© 2023 Moreira et al.
PY - 2023/9
Y1 - 2023/9
N2 - Since 2014, Brazil has experienced an unprecedented epidemic caused by chikungunya virus (CHIKV), with several waves of East-Central-South-African (ECSA) lineage transmission reported across the country. In 2018, Rio de Janeiro state, the third most populous state in Brazil, reported 41% of all chikungunya cases in the country. Here we use evolutionary and epidemiological analysis to estimate the timescale of CHIKV-ECSA-American lineage and its epidemiological patterns in Rio de Janeiro. We show that the CHIKV-ECSA outbreak in Rio de Janeiro derived from two distinct clades introduced from the Northeast region in mid-2015 (clade RJ1, n = 63/67 genomes from Rio de Janeiro) and mid-2017 clade RJ2, n = 4/67). We detected evidence for positive selection in non-structural proteins linked with viral replication in the RJ1 clade (clade-defining: nsP4-A481D) and the RJ2 clade (nsP1-D531G). Finally, we estimate the CHIKV-ECSA’s basic reproduction number (R0) to be between 1.2 to 1.6 and show that its instantaneous reproduction number (Rt) displays a strong seasonal pattern with peaks in transmission coinciding with periods of high Aedes aegypti transmission potential. Our results highlight the need for continued genomic and epidemiological surveillance of CHIKV in Brazil, particularly during periods of high ecological suitability, and show that selective pressures underline the emergence and evolution of the large urban CHIKV-ECSA outbreak in Rio de Janeiro.
AB - Since 2014, Brazil has experienced an unprecedented epidemic caused by chikungunya virus (CHIKV), with several waves of East-Central-South-African (ECSA) lineage transmission reported across the country. In 2018, Rio de Janeiro state, the third most populous state in Brazil, reported 41% of all chikungunya cases in the country. Here we use evolutionary and epidemiological analysis to estimate the timescale of CHIKV-ECSA-American lineage and its epidemiological patterns in Rio de Janeiro. We show that the CHIKV-ECSA outbreak in Rio de Janeiro derived from two distinct clades introduced from the Northeast region in mid-2015 (clade RJ1, n = 63/67 genomes from Rio de Janeiro) and mid-2017 clade RJ2, n = 4/67). We detected evidence for positive selection in non-structural proteins linked with viral replication in the RJ1 clade (clade-defining: nsP4-A481D) and the RJ2 clade (nsP1-D531G). Finally, we estimate the CHIKV-ECSA’s basic reproduction number (R0) to be between 1.2 to 1.6 and show that its instantaneous reproduction number (Rt) displays a strong seasonal pattern with peaks in transmission coinciding with periods of high Aedes aegypti transmission potential. Our results highlight the need for continued genomic and epidemiological surveillance of CHIKV in Brazil, particularly during periods of high ecological suitability, and show that selective pressures underline the emergence and evolution of the large urban CHIKV-ECSA outbreak in Rio de Janeiro.
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U2 - 10.1371/journal.pntd.0011536
DO - 10.1371/journal.pntd.0011536
M3 - Article
C2 - 37769008
AN - SCOPUS:85173582483
SN - 1935-2727
VL - 17
JO - PLoS neglected tropical diseases
JF - PLoS neglected tropical diseases
IS - 9 September
M1 - e0011536
ER -