Understanding the evolution and spread of chikungunya virus in the Americas using complete genome sequences

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.

Keywords: Americas; Caribbean; chikungunya virus; complete genome; evolution; selection analysis.

Figure 1.

MCC phylogeny based on the complete ORFs of 149 Asian lineage sequences (Asian149), including all Caribbean sequences. Taxon labels include year of isolation, accession number/sequence ID and country of isolation, except in collapsed clades, which are comprised of two or more sequences from the same country and year. The Asian/American lineage comprises all Caribbean sequences, including the thirty-three newly generated sequences, as well as Asian sequences from Central and South America and a 2015 sequence from French Polynesia (Genbank Accession No. KR559473). The most closely related sequences to the Asian/American lineage were sequences from American Samoa (2014), the Philippines (2013) and Micronesia (2013). Posterior probabilities ≥ 99 per cent are indicated at relevant nodes.

Figure 2.

The Asian/American lineage and its most closely related sequence from American Samoa (2014). Taxon labels include year of isolation, accession number/sequence ID and country of isolation except in collapsed clades, which are comprised of two or more sequences from the same country and year. The number of sequences in each collapsed clade is shown in parentheses, (the accession numbers for sequences in these collapsed clades are shown in Supplementary Figure S2). Amino acid changes defining clades within the phylogeny are indicated by coloured bars on the relevant branches (blue = 6K L20M and E2 V368A; red= nsP4 R99Q; green = nsP4 H179Y; orange = E2 V113A, purple = nsP3 Stop521R; pink = E1 T101M). Terminal branches of the tree are colored according to the region to which the country from which the sequence at the tip was derived, i.e. Central America (Mexico); Greater Antilles (Cayman Islands, Dominican Republic, Haiti, Jamaica, Puerto Rico); Leeward Islands (Anguilla, Antigua, British Virgin Islands, Guadeloupe, Montserrat, Saint Barthélemy, St. Kitts and Saint Martin); Lucayan Archipelago (Bahamas and Turks & Caicos); Oceania (American Samoa, French Polynesia, Micronesia and New Caledonia); South America (Brazil, Colombia, Guyana and Suriname); Windward Islands (Barbados, Dominica, Grenada, Martinique, St. Lucia, St. Vincent and Trinidad). Internal branches are colored according to the most probable (model) location of their parental nodes and the location state probability is indicated as a percentage at selected nodes. Also at two selected nodes, in square brackets, are node ages. and corresponding 95% HPDs. Nodes with posterior probabilities (clade credibilities) ≥0.99 are labelled.