Sequencing of isolates from patients in Bahia, Brazil, where most Zika virus cases in Brazil have been reported, resulted in 11 whole and partial Zika virus genomes. Phylogenetic analyses revealed a well-supported Bahia-specific Zika virus lineage, which indicates sustained Zika virus circulation in Salvador, Bahia's capital city, since mid-2014.
Keywords: Bahia; Brazil; ZIKV; Zika virus; capture probe enrichment; flaviviruses; metagenomic next-generation sequencing; molecular clock; mosquito-borne infections; outbreak surveillance; phylogenetic analysis; vector-borne infections; viral genome assembly; viruses.