Virologica Sinica

, Volume 31, Issue 2, pp 118–130 | Cite as

Phylogenetic analysis revealed the central roles of two African countries in the evolution and worldwide spread of Zika virus

  • Shu Shen
  • Junming Shi
  • Jun Wang
  • Shuang Tang
  • Hualin Wang
  • Zhihong Hu
  • Fei DengEmail author
Research Article


Recent outbreaks of Zika virus (ZIKV) infections in Oceania's islands and the Americas were characterized by high numbers of cases and the spread of the virus to new areas. To better understand the origin of ZIKV, its epidemic history was reviewed. Although the available records and information are limited, two major genetic lineages of ZIKV were identified in previous studies. However, in this study, three lineages were identified based on a phylogenetic analysis of all virus sequences from GenBank, including those of the envelope protein (E) and non-structural protein 5 (NS5) coding regions. The spatial and temporal distributions of the three identified ZIKV lineages and the recombination events and mechanisms underlying their divergence and evolution were further elaborated. The potential migration pathway of ZIKV was also characterized. Our findings revealed the central roles of two African countries, Senegal and Cote d'Ivoire, in ZIKV evolution and genotypic divergence. Furthermore, our results suggested that the outbreaks in Asia and the Pacific islands originated from Africa. The results provide insights into the geographic origins of ZIKV outbreaks and the spread of the virus, and also contribute to a better understanding of ZIKV evolution, which is important for the prevention and control of ZIKV infections.


Flaviviridae Zika virus (ZIKV) phylogenetic analysis lineages recombination migration 


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Copyright information

© Wuhan Institute of Virology, CAS and Springer Science+Business Media Singapore 2016

Authors and Affiliations

  • Shu Shen
    • 1
  • Junming Shi
    • 1
  • Jun Wang
    • 1
  • Shuang Tang
    • 1
  • Hualin Wang
    • 1
  • Zhihong Hu
    • 1
  • Fei Deng
    • 1
    Email author
  1. 1.State Key Laboratory of Virology, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina

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