Emergence and persistence of the Chikungunya virus East-Central-South-African genotype in Northeast Brazil

Summary We investigate an outbreak of exanthematous illness in Maceió, Alagoas, using molecular surveillance. Of 273 samples, 76% tested RT-qPCR positive for Chikungunya virus. Phylogenetic analysis reveals that the outbreak was caused by the East-Central-South-African genotype, and that this lineage has likely persisted since mid-2014 in Northeast Brazil. Article summary line Transmission of the Chikungunya virus East-Central-South-African genotype has been ongoing in the Northeast region of Brazil since mid-2014.