Following in the Footsteps of the Chikungunya Virus in Brazil: The First Autochthonous Cases in Amapá in 2014 and Its Emergence in Rio de Janeiro during 2016

Abstract

Currently, Brazil lives a triple arboviruses epidemic (DENV, ZIKV and CHIKV) making the differential diagnosis difficult for health professionals. Here, we aimed to investigate chikungunya cases and the possible occurrence of co-infections during the epidemic in Amapá (AP) that started in 2014 when the first autochthonous cases were reported and in Rio de Janeiro (RJ) in 2016. We further performed molecular characterization and genotyping of representative strains. In AP, 51.4% of the suspected cases were confirmed for CHIKV, 71.0% (76/107). Of those, 24 co-infections by CHIKV/DENV, two by CHIKV/DENV-1, and two by CHIKV/DENV-4 were observed. In RJ, 76.9% of the suspected cases were confirmed for CHIKV and co-infections by CHIKV/DENV (n = 8) and by CHIKV/ZIKV (n = 17) were observed. Overall, fever, arthralgia, myalgia, prostration, edema, exanthema, conjunctival hyperemia, lower back pain, dizziness, nausea, retroorbital pain, and anorexia were the predominating chikungunya clinical symptoms described. All strains analyzed from AP belonged to the Asian genotype and no amino acid changes were observed. In RJ, the East-Central-South-African genotype (ECSA) circulation was demonstrated and no E1-A226V mutation was observed. Despite this, an E1-V156A substitution was characterized in two samples and for the first time, the E1-K211T mutation was reported in all samples analyzed.

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

“…Despite its synchronicity, there is still limited information about the genomic epidemiology of CHIKV during the Brazilian epidemics. To provide more information about the dynamics of CHIKV epidemics in Brazil, we generated 23 new near-complete genome sequences from Rio de Janeiro that had the first detection of CHIKV in 2016 and experienced an explosive outbreak in 2019 [10,[12][13][14].…”

“…A year later, in 2014, in Brazil, the co-circulation of the Asian and ECSA genotypes were reported in Northern and Northeastern, respectively [8,9]. Since then, the ECSA genotype has been detected in several other Brazilian states in the northeastern, southeastern, and northern regions, exerting a serious threat to public health [10][11][12][13][14][15][16][17].…”

The phylogenetic approach for viral infectious disease evolution and epidemiology: An updating review

“…The application of Bayesian statistical inference framework, can allow the reconstruction of the geographic history of the still ongoing and never reported before epidemic on the basis of the first isolates sampled at known times . It has been showed that CHIKV was imported to the Americas from South‐East Asia …”

“…180 It has been showed that CHIKV was imported to the Americas from South-East Asia. [181][182][183][184][185] During CHIKV outbreak in 2005 and 2006, nonsynonymous mutation (A226V) occurred both on La Reunion and in some Indian CICCOZZI ET AL.…”

Spatio-temporal modelling of the first Chikungunya epidemic in an intra-urban setting: the role of socioeconomic status, environment and temperature

“…The first chikungunya virus (CHIKV) epidemic in Rio de Janeiro city, the second most populated city in Brazil and its main tourist destination, occurred in 2016 (de Souza et al, 2018).…”