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Randomized Controlled Trial
. 2019 Jun 11;14(6):e0217871.
doi: 10.1371/journal.pone.0217871. eCollection 2019.

Circulation of chikungunya virus East/Central/South African lineage in Rio de Janeiro, Brazil

Joilson Xavier  1   2 , Marta Giovanetti  2   3 , Vagner Fonseca  3   4 , Julien Thézé  5 , Tiago Gräf  6 , Allison Fabri  2   6 , Jaqueline Goes de Jesus  1 , Marcos Cesar Lima de Mendonça  2 , Cintia Damasceno Dos Santos Rodrigues  2 , Maria Angélica Mares-Guia  2 , Carolina Cardoso Dos Santos  2 , Stephane Fraga de Oliveira Tosta  3 , Darlan Candido  5 , Rita Maria Ribeiro Nogueira  2 , André Luiz de Abreu  7 , Wanderson Kleber Oliveira  7 , Carlos F Campelo de Albuquerque  8 , Alexandre Chieppe  9 , Tulio de Oliveira  4 , Patrícia Brasil  10 , Guilherme Calvet  10 , Patrícia Carvalho Sequeira  2 , Nuno Rodrigues Faria  5 , Ana Maria Bispo de Filippis  2 , Luiz Carlos Junior Alcantara  2   3
Affiliations
Randomized Controlled Trial

Circulation of chikungunya virus East/Central/South African lineage in Rio de Janeiro, Brazil

Joilson Xavier et al. PLoS One. .

Abstract

The emergence of chikungunya virus (CHIKV) has raised serious concerns due to the virus' rapid dissemination into new geographic areas and the clinical features associated with infection. To better understand CHIKV dynamics in Rio de Janeiro, we generated 11 near-complete genomes by means of real-time portable nanopore sequencing of virus isolates obtained directly from clinical samples. To better understand CHIKV dynamics in Rio de Janeiro, we generated 11 near-complete genomes by means of real-time portable nanopore sequencing of virus isolates obtained directly from clinical samples. Our phylogenetic reconstructions indicated the circulation of the East-Central-South-African (ECSA) lineage in Rio de Janeiro. Time-measured phylogenetic analysis combined with CHIKV notified case numbers revealed the ECSA lineage was introduced in Rio de Janeiro around June 2015 (95% Bayesian credible interval: May to July 2015) indicating the virus was circulating unnoticed for 5 months before the first reports of CHIKV autochthonous transmissions in Rio de Janeiro, in November 2015. These findings reinforce that continued genomic surveillance strategies are needed to assist in the monitoring and understanding of arbovirus epidemics, which might help to attenuate public health impact of infectious diseases.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Molecular clock phylogeny of the CHIKV circulating in Rio de Janeiro state.
Molecular clock phylogeny obtained using 11 new CHIKV near-complete genomic sequences from the 2016–2018 epidemic in Rio de Janeiro, including 48 publicly available Brazilian CHIKV-ECSA lineage sequences. Numbers along branches represent clade posterior probability >0.90. Colours represent different locations.
Fig 2
Fig 2. Map of the state of Rio de Janeiro.
The state of Rio de Janeiro is located in south-eastern region of Brazil and its municipalities, where samples from this study were collected, are coloured in the map (see legend). Red circles indicate sampling locations of the isolates generated in this study. Map was generated by QGIS v3 software.
Fig 3
Fig 3. Weekly notified Chikungunya fever cases in the north-eastern and south-eastern regions of Brazil, 2015–2018.
Number of chikungunya fever cases by epidemiological week registered in the north-eastern and south-eastern regions of Brazil between 2015 and 2018. Epidemic curves are coloured according to geographical region (see legend). Number of cases from the state of Rio de Janeiro alone is represented by the green curve and it is not computed in the curve from southeast. Chart was generated by R software.
See this image and copyright information in PMC

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