Dated phylogenetic reconstruction of CHIKV including Brazilian genomes. The genotypes involved in autochthonous Brazilian transmission in Oiapoque and Feira de Santana are highlighted in blue (A) and red (B), respectively. On the right, isolates sampled in Feira de Santana and Oiapoque are depicted as red and blue circles, whilst isolates from the Caribbean outbreak are shown in grey circles. The inset shows the posterior density of the age of the most recent common ancestor (MRCA) of the Caribbean outbreak (A, grey) and the Feira de Santana cluster (B, red). The arrows highlight the dates of the first notifications of CHIKV cases in the Caribbean and in Feira de Santana, respectively. The index case of the ECSA genotype in Brazil arrived in Feira de Santana in June (grey bar). A ML tree with tip information can be found in Additional file 1: Figure S1.