Spread of Chikungunya Virus East/Central/South African Genotype in Northeast Brazil

Abstract

We investigated an outbreak of exanthematous illness in Maceió by using molecular surveillance; 76% of samples tested positive for chikungunya virus. Genetic analysis of 23 newly generated genomes identified the East/Central/South African genotype, suggesting that this lineage has persisted since mid-2014 in Brazil and may spread in the Americas and beyond.

Keywords: Brazil; ECSA genotype; East/Central/South African genotype; Maceió; Zika virus; chikungunya virus; dengue virus; genetic epidemiology; vector-borne infections; viruses.

Figure

Epidemiologic and genetic surveillance of CHIKV in Northeast Brazil. A) Notified CHIKV cases for Alagoas state (Maceió municipality), Paraíba state (João Pessoa municipality), and Feira de Santana (FSA) and Salvador (SAL) municipalities (3), both located in the Bahia state. B) Molecular clock phylogeny obtained using 23 novel CHIKV sequences (with length >4,000 nt) collected in Northeast Brazil (dashed box). Numbers along branches represent clade posterior probability >0.75. Colors in branches represent most probable locations. At each node, size of the colored circles is proportional to location posterior probability. Inset shows a maximum-likelihood phylogeny with all publicly available CHIKV genome sequences (n = 659). The Indian Ocean Lineage (IOL) genotype has been collapsed. Triangles represent clades circulating in the Americas; the American-ECSA lineage reported in this study is shown in red and the American-Asian lineage in blue. CHIKV, chikungunya virus; ECSA, East/Central/South African genotype; WAfr, West African genotype.