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Sahadeo NSD, Allicock OM, De Salazar PM, Auguste AJ, Widen S, Olowokure B, Gutierrez C, Valadere AM, Polson-Edwards K, Weaver SC, Carrington CVF. Understanding the evolution and spread of chikungunya virus in the Americas using complete genome sequences. Virus Evol 2017; 3:vex010. [PMID: 28480053 PMCID: PMC5413804 DOI: 10.1093/ve/vex010] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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 islands, 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 outbreak, forming an 'Asian/American' lineage defined by two amino acid substitutions, E2 V368A and 6K L20M, and divided into two well-supported clades. This lineage is estimated to be evolving at a mean rate of 5 × 10-4 substitutions per site per year (95% higher probability density, 2.9-7.9 × 10-4) and to have arisen from an ancestor introduced to the Caribbean (most likely from Oceania) in about March 2013, 9 months prior to the first report of CHIKV in the Americas. Estimation of evolutionary rates for individual gene regions and selection analyses indicate that (in contrast to the Indian Ocean Lineage that emerged from the ECSA genotype followed by adaptive evolution and with a significantly higher substitution rate) the evolutionary dynamics of the Asian/American lineage are very similar to the rest of the Asian genotype and natural selection does not appear to have played a major role in its emergence. However, several codon sites with evidence of positive selection were identified within the non-structural regions of Asian genotype sequences outside of the Asian/American lineage.
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Affiliation(s)
- N S D Sahadeo
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine Campus, Trinidad and Tobago
| | - O M Allicock
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine Campus, Trinidad and Tobago
| | - P M De Salazar
- Caribbean Public Health Agency, Port-of-Spain, Trinidad and Tobago.,ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - A J Auguste
- Institute for Human Infections and Immunity and Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - S Widen
- Institute for Human Infections and Immunity and Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - B Olowokure
- Caribbean Public Health Agency, Port-of-Spain, Trinidad and Tobago
| | - C Gutierrez
- Caribbean Public Health Agency, Port-of-Spain, Trinidad and Tobago
| | - A M Valadere
- Caribbean Public Health Agency, Port-of-Spain, Trinidad and Tobago
| | - K Polson-Edwards
- Caribbean Public Health Agency, Port-of-Spain, Trinidad and Tobago
| | - S C Weaver
- Institute for Human Infections and Immunity and Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - C V F Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine Campus, Trinidad and Tobago
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