Co-Circulation of Two Independent Clades and Persistence of CHIKV-ECSA Genotype during Epidemic Waves in Rio de Janeiro, Southeast Brazil

• Main Authors: Allison Araújo Fabri, Cintia Damasceno dos Santos Rodrigues, Carolina Cardoso dos Santos, Flávia Löwen Levy Chalhoub, Simone Alves Sampaio, Nieli Rodrigues da Costa Faria, Maria Celeste Torres, Vagner Fonseca, Patricia Brasil, Guilherme Calvet, Luiz Carlos Junior Alcantara, Ana Maria Bispo de Filippis, Marta Giovanetti, Fernanda de Bruycker-Nogueira
• Format: Article
• Language: English
• Published: MDPI AG 2020-11-01
• Series: Pathogens
• Subjects: chikungunya virus; ECSA genotype; persistence; co-circulation; rio de janeiro; Brazil
• Online Access: https://www.mdpi.com/2076-0817/9/12/984

The Chikungunya virus infection in Brazil has raised several concerns due to the rapid dissemination of the virus and its association with several clinical complications. Nevertheless, there is limited information about the genomic epidemiology of CHIKV circulating in Brazil from surveillance studies. Thus, to better understand its dispersion dynamics in Rio de Janeiro (RJ), one of the most affected states during the 2016–2019 epidemic waves, we generated 23 near-complete genomes of CHIKV isolates from two main cities located in the metropolitan mesoregion, obtained directly from clinical samples. Our phylogenetic reconstructions suggest the 2019-CHIKV-ECSA epidemic in RJ state was characterized by the co-circulation of multiple clade (clade A and B), highlighting that two independent introduction events of CHIKV-ECSA into RJ state have occurred between 2016–2019, both mediated from the northeastern region. Interestingly, we identified that the two-clade displaying eighteen characteristic amino acids changes among structural and non-structural proteins. Our findings reinforce that genomic data can provide information about virus genetic diversity and transmission dynamics, which might assist in the arbovirus epidemics establishing of an effective surveillance framework.