Abstract
Zika virus (ZIKV) has caused explosive epidemics in the Pacific and the Americas, posing a serious threat to public health. Conventional opinion advocates that ZIKV evolved into two distinct lineages, namely, African and Asian. Descendants of this latter lineage dispersed globally causing major epidemics. However, based on shared amino acid replacements and phylogenetic analyses, it was recently contentiously proposed that the Asian lineage was a direct descendant of the African lineage. To address this contentious issue, we reconstructed a phylogenetic tree of ZIKV using the method based on shared amino acid replacements and found that ZIKV evolved into two distinct lineages. This supports the conventional phylogenetic divergence pattern of ZIKV. Evidence of recombination and sequencing errors was identified among the large collection of ZIKV. As such problematic sequences could confound the phylogenetic analyses, they were removed. Bayesian phylogenetic analyses using the improved sequence data enabled estimates for the divergence time in the past of the African and Asian lineages of ∼180 years ago. Moreover, we found that the Asian lineage viruses did not evolve at an elevated rate. Our findings provide additional support for the conventional opinion that the Asian lineage of ZIKV diverged from the African lineage.