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

• Main Authors: Joilson Xavier, Marta Giovanetti, Vagner Fonseca, Julien Thézé, Tiago Gräf, Allison Fabri, Jaqueline Goes de Jesus, Marcos Cesar Lima de Mendonça, Cintia Damasceno Dos Santos Rodrigues, Maria Angélica Mares-Guia, Carolina Cardoso Dos Santos, Stephane Fraga de Oliveira Tosta, Darlan Candido, Rita Maria Ribeiro Nogueira, André Luiz de Abreu, Wanderson Kleber Oliveira, Carlos F Campelo de Albuquerque, Alexandre Chieppe, Tulio de Oliveira, Patrícia Brasil, Guilherme Calvet, Patrícia Carvalho Sequeira, Nuno Rodrigues Faria, Ana Maria Bispo de Filippis, Luiz Carlos Junior Alcantara
• Format: Article
• Language: English
• Published: Public Library of Science (PLoS) 2019-01-01
• Series: PLoS ONE
• Online Access: https://doi.org/10.1371/journal.pone.0217871

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.