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

Abstract

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.

Genomic Epidemiology Reveals the Circulation of the Chikungunya Virus East/Central/South African Lineage in Tocantins State, North Brazil

“…Our phylogenetic analysis placed the genomes to the ECSA genotype. This lineage has been reported as predominant in the Southeast and Northeast Region of Brazil, respectively [ 12 , 36 , 37 , 38 , 39 ]. Naveca et al [ 40 ] reported the introduction of the ECSA lineage in Roraima in the North Region of Brazil, and de Castro et al reported the ESCA circulation in the Paraná state in the South Region of Brazil.…”

Was It Chikungunya? Laboratorial and Clinical Investigations of Cases Occurred during a Triple Arboviruses’ Outbreak in Rio de Janeiro, Brazil

“…According to Fabri et al (2020), since 2015, two independent CHIKV-ECSA genotype introductions occurred in RJ, both from Brazil's northeastern region [67]. The first report and characterization of CHIKV-ECSA in RJ occurred in 2016 [68].…”

Insights into Antibody-Mediated Alphavirus Immunity and Vaccine Development Landscape

“…Nonetheless, given that the ECSA lineage was responsible for the ongoing outbreak at the time of development, the high degree of amino acid similarity between the two CHIKV strains suggested that the vaccine would be protective against viruses of other genotypes. However, it would have been curious to characterize a VLP produced from a CHIKV strain of the ECSA lineage, given that it is the strain responsible for recent Chikungunya epidemics all around the world [ 119 , 120 , 121 , 122 , 123 ].…”

“…Data curated from literature reported through February 2021. Numbers in superscript refer to reference numbers (See Reference list [ 23 , 73 , 114 , 115 , 116 , 117 , 118 , 119 , 120 , 121 , 122 , 123 , 124 , 125 , 126 , 127 , 128 , 129 , 130 , 131 , 132 , 133 , 134 , 135 , 136 , 137 , 138 , 139 , 140 , 141 , 142 , 143 , 144 , 145 , 146 , 147 , 148 , 149 , 150 , 151 , 152 , 153 , 154 , 155 , 156 , 157 , 158 , 159 ,…”