The Asian Lineage of Zika Virus: Transmission and Evolution in Asia and the Americas

Abstract

Since first isolation in 1947 from the Zika forest in Uganda, Zika virus (ZIKV) has been principally known as a benign agent associated with sporadic human infections in a restricted number of African countries. However, during 2015-2016, an Asian lineage of ZIKV caused an unprecedentedly large outbreak in the Americas and sizeable numbers of exported cases across the globe. In this review, we critically appraise the recent advances in molecular epidemiological studies of ZIKV performed to date, and we highlight the pivotal role played by genomic surveillance in elucidating the origins, dissemination and evolution of the Asian lineage of ZIKV in Asia and in the Americas.

Keywords: Asian lineage; Evolution; R e; Transmission; Zika virus (ZIKV).

Fig. 1

Phylogeny and molecular characterization of the Asian lineage of ZIKV. Full-length ZIKV genomes (n = 448) derived from the Asian lineage were assembled and a phylogenetic analysis using BEAST 1.8.4 was performed (Drummond et al.2012). The GTR + Γ nucleotide model was applied to account for rate variation among sites, with four categories for the Γ distribution. A log-normal distributed relaxed molecular clock was employed and the Bayesian skyline coalescent was designated as the tree prior. A Markov chain Monte Carlo with one hundred million steps was run twice independently and the first 10% were removed as burn-in. The posterior probability distribution of the parameters and trees from the two independent runs was combined using LogCombiner embedded in BEAST 1.8.4. Viruses identified from the ZIKV African lineage and from Indonesia cases in 1966 were also downloaded and phylogenetically analyzed using Maximum Likelihood. In the African lineage, one strain, ArD142623 (GenBank No. KF3838120), had a long branch length, which is displayed using a dashed line. In the Asian lineage, tips with circles represent confirmed ZIKV imported cases. Line color represents the collection site of the virus and the classification of the countries into different regions was based on Wikipedia (https://www.wikipedia.org/). In the right panel, different colors represent different amino acids, which have been shown in the legend in the bottom right of the panel.

Fig. 2

Effective reproductive number (R_e) of ZIKV of the Asian lineage through time. The effective reproductive number (R_e) was estimated using a birth–death skyline approach implemented in BEAST 2 with ZIKVs identified since 2013. An uncorrelated log-normal relaxed clock model and the GTR + Γ nucleotide substitution model were used. A Markov chain Monte Carlo was run with one hundred million steps and the first 10% were removed as burn-in. In the serially sampled birth–death skyline model, the priors for the molecular clock rate, R_e, the sampling proportion, and the rate at which patients recover were set according to a previous study, which were also supported by an alternative approach allowing for sampling heterogeneity (data not shown) (Thézé et al.2018). The red line and lighter shading represented the median posterior estimate of R_e and its 95% highest posterior density credible intervals, respectively. This figure was created using the R-package bdskytools (available at https://github.com/laduplessis/bdskytools).