Background: Zika virus (ZIKV) has significant potential to cause future outbreaks due to insufficient countermeasures. The evolution of ZIKV in Southeast Asian countries remains poorly understood. Materials and Methods: The phylogenetic, phylogeographic network, and recombination analyses of 366 ZIKV complete genome sequences identified between 1947 and 2021 were performed and the amino acid variation landscape was determined to reveal the evolutionary characteristics. Results: ZIKV falls into two major genogroups: GI and GII, segregated into further subgenogroups (GI-1 to GI-3) and (GII-1 to GII-3), respectively. Importantly, Thailand strains cluster with Southeast Asian outbreak strains (Singapore 2016, the Philippines 2012, Cambodia 2010) into GII-2 and form a lineage independent of French Polynesia and the Americas large outbreak strains. Thailand ZIKV strains shared their ancestral route to the strains from French Polynesia, which further connects to Brazil ZIKV through a short mutational branch. Both recombination and specific mutations may contribute to the emergence of new virus lineage in Thailand. Conclusion: This report provides insights into the evolutionary characteristics of ZIKV in Southeast Asia, which may be helpful for epidemiological investigation, vaccine development, and surveillance of the virus.
Keywords: B cell epitopes; Thailand; Zika virus; evolutionary connection; recombination; vector-borne disease.