Genome-scale phylogenetic analyses of chikungunya virus reveal independent emergences of recent epidemics and various evolutionary rates

Abstract

Chikungunya virus (CHIKV), a mosquito-borne alphavirus, has traditionally circulated in Africa and Asia, causing human febrile illness accompanied by severe, chronic joint pain. In Africa, epidemic emergence of CHIKV involves the transition from an enzootic, sylvatic cycle involving arboreal mosquito vectors and nonhuman primates, into an urban cycle where peridomestic mosquitoes transmit among humans. In Asia, however, CHIKV appears to circulate only in the endemic, urban cycle. Recently, CHIKV emerged into the Indian Ocean and the Indian subcontinent to cause major epidemics. To examine patterns of CHIKV evolution and the origins of these outbreaks, as well as to examine whether evolutionary rates that vary between enzootic and epidemic transmission, we sequenced the genomes of 40 CHIKV strains and performed a phylogenetic analysis representing the most comprehensive study of its kind to date. We inferred that extant CHIKV strains evolved from an ancestor that existed within the last 500 years and that some geographic overlap exists between two main enzootic lineages previously thought to be geographically separated within Africa. We estimated that CHIKV was introduced from Africa into Asia 70 to 90 years ago. The recent Indian Ocean and Indian subcontinent epidemics appear to have emerged independently from the mainland of East Africa. This finding underscores the importance of surveillance to rapidly detect and control African outbreaks before exportation can occur. Significantly higher rates of nucleotide substitution appear to occur during urban than during enzootic transmission. These results suggest fundamental differences in transmission modes and/or dynamics in these two transmission cycles.

FIG. 1.

Distribution of the CHIKV strains used in this study. The map, based on a world map template from http://www.presentationmagazine.com, was edited with permission.

FIG. 2.

Maximum clade credibility (MCC) tree of 80 CHIKV strains. The four major lineages are highlighted with different branch colors, with the sample origin highlighted by the corresponding color. The estimated 95% HPD values for most recent common ancestors are labeled beside the node and are also indicated by the thick blue horizontal node bars. The numbers adjacent to nodes indicate Bayesian posterior probability values. For clarity, the 2004 to 2009 epidemic clade is shown enlarged in the inset at upper left. Sequences with internal poly(A) insertion in the 3′UTR are marked with an asterisk (*). Strains are labeled as follows: location_strain name_date (year) of collection.

FIG. 3.

Differences in the extrinsic incubation time may lead to different apparent rates of evolution. A model is depicted demonstrating how differences in vertebrate host density, availability, or herd immunity might lead to a longer extrinsic incubation time for the virus in enzootic mosquitoes, leading to less replication in the enzootic mosquitoes and resulting in the observed differences in the rate of nucleotide substitutions between enzootic and urban transmission cycles. This model assumes (i) a minimum extrinsic incubation of 1 week (blue arrows), (ii) an average intrinsic incubation (in vertebrates) of 2 days (green arrows), and (iii) downregulation of viral replication in the mosquito after 1 week (dashed arrow). (Upper panel) Sylvatic/enzootic circulation. Enzootic CHIKV is transmitted among sparsely populated or high herd immunity primates, so an infected mosquito is likely to downregulate viral replication before finding a subsequent blood-meal from a susceptible host. Less replication in a given time period results in slower evolution. (Lower panel) Urban circulation. The higher density of both competent vectors and susceptible humans that occurs in areas of urban CHIKV transmission results in more frequent transmission, meaning that an infected mosquito is likely to transmit before it downregulates viral replication. This could result in more viral RNA replication in serially infected hosts in a given time period, leading to faster evolution.