title: First Report of the East-Central South African Genotype of Chikungunya Virus in Rio de Janeiro, Brazil.
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.
authors.affiliation: Viral Immunology Laboratory, Oswaldo Cruz Institute, Rio de Janeiro, Brazil.
authors.forename: Thiara Manuele Alves
authors.initials: TM
authors.lastname: Souza
authors.affiliation: Viral Immunology Laboratory, Oswaldo Cruz Institute, Rio de Janeiro, Brazil.
authors.forename: Elzinandes Leal
authors.initials: EL
authors.lastname: Azeredo
authors.affiliation: Viral Immunology Laboratory, Oswaldo Cruz Institute, Rio de Janeiro, Brazil.
authors.forename: Jessica
authors.initials: J
authors.lastname: Badolato-Corrêa
authors.affiliation: Rio-Laranjeiras Hospital, Gaffrée Guinle University Hospital (Federal University of the State of Rio de Janeiro), Rio de Janeiro, Brazil Pedro Ernesto University Hospital (University of the State of Rio de Janeiro), Rio de Janeiro, Brazil.
authors.forename: Paulo Vieira
authors.initials: PV
authors.lastname: Damasco
authors.affiliation: Rio-Laranjeiras Hospital, Rio de Janeiro, Brazil.
authors.forename: Carla
authors.initials: C
authors.lastname: Santos
authors.affiliation: Viral Immunology Laboratory, Oswaldo Cruz Institute, Rio de Janeiro, Brazil.
authors.forename: Fabienne
authors.initials: F
authors.lastname: Petitinga-Paiva
authors.affiliation: Viral Immunology Laboratory, Oswaldo Cruz Institute, Rio de Janeiro, Brazil.
authors.forename: Priscila Conrado Guerra
authors.initials: PC
authors.lastname: Nunes
authors.affiliation: Viral Immunology Laboratory, Oswaldo Cruz Institute, Rio de Janeiro, Brazil; UFRJ- Federal University of Rio de Janeiro, Laboratory of Genetics, IPPMG - Martagão Gesteira Child Care and Pediatrics Institute, Rio de Janeiro, Brazil.
authors.forename: Luciana Santos
authors.initials: LS
authors.lastname: Barbosa
authors.affiliation: Viral Immunology Laboratory, Oswaldo Cruz Institute, Rio de Janeiro, Brazil.
authors.forename: Márcio Costa
authors.initials: MC
authors.lastname: Cipitelli
authors.affiliation: Viral Immunology Laboratory, Oswaldo Cruz Institute, Rio de Janeiro, Brazil. Mosquitoes Laboratory, Oswaldo Cruz Institute, Rio de Janeiro, Brazil.
authors.forename: Thais
authors.initials: T
authors.lastname: Chouin-Carneiro
authors.affiliation: Viral Immunology Laboratory, Oswaldo Cruz Institute, Rio de Janeiro, Brazil.
authors.forename: Nieli Rodrigues Costa
authors.initials: NR
authors.lastname: Faria
authors.affiliation: Flavivirus Laboratory, Oswaldo Cruz Institute, Rio de Janeiro, Brazil.
authors.forename: Rita Maria Ribeiro
authors.initials: RM
authors.lastname: Nogueira
authors.affiliation: Viral Immunology Laboratory, Oswaldo Cruz Institute, Rio de Janeiro, Brazil.
authors.forename: Fernanda
authors.initials: F
authors.lastname: de Bruycker-Nogueira
authors.affiliation: Viral Immunology Laboratory, Oswaldo Cruz Institute, Rio de Janeiro, Brazil.
authors.forename: Flavia Barreto
authors.initials: FB
authors.lastname: Dos Santos
keywords: Brazil; Chikungunya; ECSA genotype; Rio de Janeiro; Surveillance