Phylogenetic tree of the complete genome sequence (A) and polymorphisms in E1 and E2 envelope glycoproteins (B).

A) Phylogenetic tree of the complete genome sequence of the isolate CHIKV/ITA/Lazio-INMI1-2017 obtained from the current outbreak, Lazio region, Italy. The Maximum-likelihood phylogenetic tree was built with the complete genome sequence of the isolate CHIKV/ITA/Lazio-INMI1-2017 (outlined in bold characters) in the context of whole genome sequences representing the 3 major described CHIKV lineages: ECSA (including the Indian Ocean lineage), Asia and Caribbean, and West Africa. These sequences are indicated with their accession number, geographic origin and year of sampling. Asian and Caribbean and West Africa sequences are collapsed to increase the clarity of the figure. Bootstraps were generated using 1,000 replicates; only those >80 are shown. The bar represents genetic distance (substitutions per nucleotide position). B) Polymorphisms in E1 and E2 envelope glycoproteins of CHIKV/ITA/Lazio-INMI1-2017, at positions considered relevant for vector adaptation.