Phylogeny of CHIKVs causing the outbreak in the French Caribbean Islands, 2013-2014. Complete concatenated nucleotide coding sequences of CHIKV belonging to the Asian genotype were obtained by using Ion Torrent next-generation sequencing (Life Technologies) and aligned according to the amino acid sequence. Mega6 software was used to select the best-fit model for the analysis (generalized time reversible model of nucleotide substitution with a gamma distributed rate variation among sites) and to infer a phylogenetic tree using the maximum likelihood method followed by a bootstrap analysis (1000 replicates; values above 70% indicated).¹⁰  Sequence information for each virus corresponds to virus strain name (according to GenBank nomenclature) followed by date and country of isolation. The tree was rooted by using a sequence belonging to the East Central South African lineage (LR2006_OPY1 2006 Reunion).