Zika virus (ZIKV) is a mosquito-borne flavivirus. It was first isolated from Uganda in 1947 and has become an
emergent event since 2007. However, because of the inconsistency of alignment methods, the evolution of
ZIKV remains poorly understood. In this study, we first use the complete protein and an alignment-free method
to build a phylogenetic tree of 87 Zika strains in which Asian, East African, and West African lineages are
characterized. We also use the NS5 protein to construct the genetic relationship among 44 Zika strains. For the
first time, these strains are divided into two clades: African 1 and African 2. This result suggests that ZIKV
originates from Africa, then spread to Asia, Pacific islands, and throughout the Americas. We also perform the
phylogeny analysis for 53 viruses in genus Flavivirus to which ZIKV belongs using complete proteins. Our
conclusion is consistent with the classification by the hosts and transmission vectors.