Zika and Flaviviruses Phylogeny Based on the Alignment-Free Natural Vector Method

Area of Science:

• Virology
• Molecular Biology
• Epidemiology

Background:

• Zika virus (ZIKV), a mosquito-borne flavivirus, first isolated in 1947, has emerged globally since 2007.
• Previous studies on ZIKV evolution are hindered by inconsistent alignment methods, leading to an incomplete understanding of its genetic diversity and spread.

Purpose of the Study:

• To elucidate the evolutionary history and phylogenetic relationships of Zika virus strains.
• To characterize distinct ZIKV lineages and clades using novel alignment-free methods.
• To trace the geographical origins and dissemination pathways of ZIKV.

Main Methods:

• Phylogenetic tree construction using complete protein sequences and an alignment-free approach for 87 ZIKV strains.
• Analysis of the NS5 protein to establish genetic relationships among 44 ZIKV strains, leading to the identification of two novel clades: African 1 and African 2.
• Comparative phylogenetic analysis of 53 viruses within the genus Flavivirus using complete protein sequences.

Main Results:

• Characterization of Asian, East African, and West African lineages of ZIKV.
• First-time division of ZIKV strains into two distinct clades: African 1 and African 2, suggesting an African origin.
• Phylogenetic analysis supports ZIKV's origin in Africa, followed by subsequent spread to Asia, Pacific islands, and the Americas.

Conclusions:

• The study provides a robust phylogenetic framework for understanding ZIKV evolution and geographical dissemination.
• The identification of African 1 and African 2 clades offers new insights into ZIKV's African origins and diversification.
• Findings align with existing classifications based on hosts and transmission vectors, reinforcing the proposed evolutionary trajectory of ZIKV.