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• The Brazilian sequence ZIKV lineage proportion changed across five years. • The automated surveillance system helps identify ZIKV molecular epidemiology. • A new lineage emerged in Brazil and could be a potential risk of a new epidemic. There is currently no system to track the emergence of Zika virus (ZIKV) subtypes. We developed a surveillance system able to retrieve sequence submissions and further classify distinct ZIKV genotypes in the world. This approach was able to detect a new occurrence of ZIKV from an African lineage in Brazil in 2019. [ABSTRACT FROM AUTHOR]