The Zika Virus Typing Tool: Introduction.
The definition of a Zika genotype is based on the identification of well defined phylogenetic clusters that its origin has been associated to a given geographic region.
We have carefully analysed all of ZIKV whole genomes and reviewed in the literature in order to represent the diversity of each phylotype. In addition, we performed extensive testing to be sure that our reference strains accurately classify other sequences. We found that the whole genome and the Envelope gene (E) gene to be suitable for classification
- We include 3 phylotypes
- Phylotype 1 includes sequences from deferent African countries
- Phylotype 2 includes sequences from Asian origin
- Phylotype 3 includes a recently published Senegalese whole genome, which is very divergent from other African ones (Faye et al. PLoS Negl Trop Dis 2014, 8(1): e2636)
- The phylogenies are rooted with Spondweni virus
Fig. 1. Zika virus maximum likelihood phylogenetic tree of (A) complete genome and (B) E gene