Molecular evolution of Zika virus during its emergence in the 20(th) century

Abstract

Zika virus (ZIKV) is a mosquito-borne flavivirus first isolated in Uganda in 1947. Although entomological and virologic surveillance have reported ZIKV enzootic activity in diverse countries of Africa and Asia, few human cases were reported until 2007, when a Zika fever epidemic took place in Micronesia. In the context of West Africa, the WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever at Institut Pasteur of Dakar (http://www.pasteur.fr/recherche/banques/CRORA/) reports the periodic circulation of ZIKV since 1968. Despite several reports on ZIKV, the genetic relationships among viral strains from West Africa remain poorly understood. To evaluate the viral spread and its molecular epidemiology, we investigated 37 ZIKV isolates collected from 1968 to 2002 in six localities in Senegal and Côte d'Ivoire. In addition, we included strains from six other countries. Our results suggested that these two countries in West Africa experienced at least two independent introductions of ZIKV during the 20(th) century, and that apparently these viral lineages were not restricted by mosquito vector species. Moreover, we present evidence that ZIKV has possibly undergone recombination in nature and that a loss of the N154 glycosylation site in the envelope protein was a possible adaptive response to the Aedes dalzieli vector.

Figure 1. Maximum likelihood phylogenetic tree inferred for concatenated of sequences from Envelope and NS5 genes of Zika virus.

Consensus tree summarized after 1000 non-parametric bootstrap replicates, with support values greater than 60% shown in the nodes. The cluster the Ugandan MR766 prototype strain was highlighted by the yellow sector and the Nigerian cluster was highlighted by the green sector. The strains from Senegal and Côte d'Ivoire are shown in green and orange, respectively. The tree has been rooted with the Spondweni lineage isolated in South Africa was used as outgroup to root the tree.

Figure 2. Geographic spread of ZIKV in Africa and Asia.

The directed lines connect the most probable sources and target localities of viral lineages (shown by arrows), with widths proportional to the posterior probabilities and values shown in red. Only plausible routes with probabilities above 50% are shown. The distinct introductions into Senegal and Côte d'Ivoire were represented by different colors. The estimated time to the most recent common ancestor of strains from different countries are shown with 95% posterior time intervals in parenthesis and could be interpreted as the oldest possible year of introduction of that lineage at that locality.

Figure 3. Mapping of predicted glycosylation sites on envelope protein of ZIKV.

A) Alignment of E protein showing predicted glycosylation sites. Red arrows point to O-linked glycosylation sites (Ser or Thr residues) and the yellow arrow points to the N-linked glycosylation site (Asn-X-Thr motif). B) Tridimensional structure of E protein. Red beads indicate O-linked glycosylation sites and the yellow bead indicates the unique N-linked glycosylation site.