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. 2017 Feb 14:9:ecurrents.outbreaks.4200119978d62ccaa454599cd2735727.
doi: 10.1371/currents.outbreaks.4200119978d62ccaa454599cd2735727.

First Report of the East-Central South African Genotype of Chikungunya Virus in Rio de Janeiro, Brazil

Thiara Manuele Alves Souza  1 , Elzinandes Leal Azeredo  1 , Jessica Badolato-Corrêa  1 , Paulo Vieira Damasco  2 , Carla Santos  3 , Fabienne Petitinga-Paiva  1 , Priscila Conrado Guerra Nunes  1 , Luciana Santos Barbosa  4 , Márcio Costa Cipitelli  1 , Thais Chouin-Carneiro  5 , Nieli Rodrigues Costa Faria  1 , Rita Maria Ribeiro Nogueira  6 , Fernanda de Bruycker-Nogueira  1 , Flavia Barreto Dos Santos  1
Affiliations

First Report of the East-Central South African Genotype of Chikungunya Virus in Rio de Janeiro, Brazil

Thiara Manuele Alves Souza et al. PLoS Curr. .

Abstract

Background: Chikungunya virus (CHIKV) is an arbovirus that causes an acute febrile syndrome with a severe and debilitating arthralgia. In Brazil, the Asian and East-Central South African (ECSA) genotypes are circulating in the north and northeast of the country, respectively. In 2015, the first autochthonous cases in Rio de Janeiro, Brazil were reported but until now the circulating strains have not been characterized. Therefore, we aimed here to perform the molecular characterization and phylogenetic analysis of CHIKV strains circulating in the 2016 outbreak occurred in the municipality of Rio de Janeiro.

Methods: The cases analyzed in this study were collected at a private Hospital, from April 2016 to May 2016, during the chikungunya outbreak in Rio de Janeiro, Brazil. All cases were submitted to the Real Time RT-PCR for CHIKV genome detection and to anti-CHIKV IgM ELISA. Chikungunya infection was laboratorially confirmed by at least one diagnostic method and, randomly selected positive cases (n=10), were partially sequenced (CHIKV E1 gene) and analyzed.

Results: The results showed that all the samples grouped in ECSA genotype branch and the molecular characterization of the fragment did not reveal the A226V mutation in the Rio de Janeiro strains analyzed, but a K211T amino acid substitution was observed for the first time in all samples and a V156A substitution in two of ten samples.

Conclusions: Phylogenetic analysis and molecular characterization reveals the circulation of the ECSA genotype of CHIKV in the city of Rio de Janeiro, Brazil and two amino acids substitutions (K211T and V156A) exclusive to the CHIKV strains obtained during the 2016 epidemic, were reported.

Keywords: Brazil; Chikungunya; ECSA genotype; Rio de Janeiro; Surveillance.

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Figures

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Fig. 1: Epidemiological data and clinical manifestations from the chikungunya confirmed cases (n=10) sequenced in this study.
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Fig. 2: Genotyping of CHIKV strains (n=10) identified in Rio de Janeiro during the outbreak occurred in 2016. Neighbor Joining method (A) and Maximum-Likelihood (B), both K2 parameters model, bootstrap of 1,000 replications. The CHIKV sequences analyzed are represented by black circles. CHIKV strains were named as follows: GenBank accession number (or name strain)/country/year. The O'nyong nyong virus was used as outgroup.
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Fig. 3: Analysis of the amino acid substitutions (positions 103 to 227) based on partial sequencing of the envelope 1 (E1) gene of the CHIKV ECSA genotype identified during the 2016 outbreak in Rio de Janeiro, Brazil. V: Valine; T: Treonine; K: Lisine; A: Alanine.
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