Increasing genetic diversity of Zika virus in the Latin American outbreak

Dear Editor,The spread of the emerging zoonotic arboviral agent, Zika virus (ZIKV), in the Americas and its association with congenital abnormalities,1, 2 including in utero growth restriction, pla...

and 1000 bootstrap replicates. Phylogenetic analysis and demographic reconstruction were jointly estimated using Bayesian Evolutionary Analysis by Sampling Trees v1.8, 9 using the strict and uncorrelated lognormal relaxed models, respectively. For tree priors, the Gaussian Markov random field Bayesian skyride model was used. Fifty million steps were run, and the first 10% were removed as burn-in.
A recent phylogenetic analysis based on viral envelope gene sequences has classified ZIKV into two major genetic lineages, African and Asian, and the Latin American ZIKV outbreaks segregate with the Asian lineage. 10 Our results supported the Asian lineage origins of the currently circulating ZIKV (Figures 1A and 1B; Supplementary Figure S1). Furthermore, phylogenetic analysis revealed that the Asian lineage has evolved into two major lineages with high statistical support ( Figures 1A and 1B), which we term the Oceanian and Latin American lineages. The Oceanian lineage included three imported Chinese ZIKV cases, all of whom returned from Fiji (Melanesia) and Samoa (Polynesia). This revealed an independent ZIKV lineage currently circulating in countries in Oceania.
Consistent with a previous report, 11 our results also supported a single introduction event of ZIKV to Latin America ( Figures 1A  and 1B), and the estimated time of this event was dated around mid-2013 ( Figure 1B). This was in agreement with a previous analysis of the time to the most recent common ancestor of all Brazilian genomes. 11 Soon after being imported to Latin America, ZIKV became highly diversified between late 2013 and early 2014 ( Figure 1B), which was supported by the co-existence of several minor clusters, although statistical support for some of these clusters was not very high ( Figures 1A and 1B). These results implied that the ZIKV responsible for the current outbreak in Latin America may have become phylogenetically diversified and increased in genetic diversity.
The Brazilian ZIKV genomes did not cluster together rather, they were interspersed among the trees clustering with genomes' sampled worldwide isolates, indicative of a high level of genetic diversity of ZIKV in Brazil, although whether this arose from multiple introductions to Brazil remains unknown, based on current data. 11 In addition, in the Latin American lineage, ZIKV genomes collected from 2015 and 2016 did not group together and were distributed throughout the clusters with no evidence of substantial lineage replacement ( Figures 1A and 1B). This suggests that no circulating ZIKV strain has gained significantly higher fitness over the others to become dominant.
The evidence for increasing genetic diversity was also supported by the demographic reconstruction analysis ( Figure 1C). Since late 2013, when the ZIKV that established the current epidemic in Latin America was introduced, the genetic diversity of ZIKV has gradually increased and reached its peak in approximately March or April 2015, following Although the analysis, based on the currently available data, suggested that the genetic diversity decreased slightly after September 2015 ( Figure 1C), we consider that this is potentially caused by the extremely low sampling density in Latin America. In summary, we present phylogenetic evidence of the co-circulation of two major ZIKV lineages in Oceania and Latin America. In addition, the Latin American lineage has become highly diversified. The genetic diversity of ZIKV may have been gradually increasing since late 2013 with its geographic expansion, reaching a peak in March or April 2015. Based on current evidence, no circulating strain of the ZIKV Latin American lineage has become dominant. However, it is extremely likely that the genetic diversity of ZIKV is underestimated due to the limited sequence data that are currently available for Latin America and also importantly for Oceania (Polynesia, Melanesia and Micronesia) and Southeast Asia. Improved sampling efforts in vector species and human cases from these regions will help to better elucidate the evolution of this zoonotic pathogen, assist efforts to validate robust serological and molecular diagnostic assays, and identify stable epitopes for vaccine development.