Virus Evolution, 2017, 3(1): vex010 doi: 10.1093/ve/vex010 Research article Understanding the evolution and spread of chikungunya virus in the Americas using complete genome sequences N. S. D. Sahadeo,1 O. M. Allicock,1 P. M. De Salazar,2,3 A. J. Auguste,4 S. Widen,4 B. Olowokure,2 C. Gutierrez,2 A. M. Valadere,2 K. Polson-Edwards,2 S. C. Weaver,4 and C. V. F. Carrington1,* 1Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine Campus, Trinidad and Tobago, 2Caribbean Public Health Agency, Port-of-Spain, Trinidad and Tobago, 3ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clınic-Universitat de Barcelona, Barcelona, Spain and 4Institute for Human Infections and Immunity and Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, Texas, USA *Corresponding author: E-mail:
[email protected] Abstract Local transmission of chikungunya virus (CHIKV) was first detected in the Americas in December 2013, after which it spread rapidly throughout the Caribbean islands and American mainland, causing a major chikungunya fever epidemic. Previous phylogenetic analysis of CHIKV from a limited number of countries in the Americas suggests that an Asian genotype strain was responsible, except in Brazil where both Asian and East/Central/South African (ECSA) lineage strains were detected. In this study, we sequenced thirty-three complete CHIKV genomes from viruses isolated in 2014 from fourteen Caribbean is- lands, the Bahamas and two mainland countries in the Americas. Phylogenetic analyses confirmed that they all belonged to the Asian genotype and clustered together with other Caribbean and mainland sequences isolated during the American out- break, forming an ‘Asian/American’ lineage defined by two amino acid substitutions, E2 V368A and 6K L20M, and divided into two well-supported clades.