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. 2016 Oct;22(10):1804–1807. doi: 10.3201/eid2210.152087

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This is a publication of the U.S. Government. This publication is in the public domain and is therefore without copyright. All text from this work may be reprinted freely. Use of these materials should be properly cited.

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Phylogenetic analysis of chikungunya virus (CHIKV) isolates from Yucatan, Mexico. Analysis was based on a 3,744-nt structural gene region (capsid-E3-E2-6K-E1) of 63 CHIKV isolates, including the 14 isolates from Yucatan. Sequences were aligned by using MUSCLE (11), and the tree was constructed by using the neighbor-joining algorithm as implemented in PHYLIP (12) and using ETE3 (Environment for Tree Exploration 3) (13). Isolates are identified by GenBank accession number, country, and year isolated. CHIKV isolates from the Yucatan are shown in bold. Bootstrap values were generated by using 1,000 repetitions and normalized on a scale of 0–1. Bootstrap values for select branches are shown. 6K, membrane-associated peptide; E, envelope; ECSA, East/Central/South African lineage; IOL, Indian Ocean lineage.