Genomic surveillance of the Chikungunya Virus (CHIKV) in Northeast Brazil after the first outbreak in 2014.

Introduction: We performed an epidemiological surveillance of the Chikungunya (CHIKV) lineages in Bahia after the 2014 East/Central/South African (ECSA) genotype outbreak.

Methods: Reverse-transcription polymerase chain reaction (RT-PCR), viral isolation, and phylogenetic analyses were conducted on serum samples from 605 patients with CHIKV-like symptoms during 2014-2018.

Results: Of the 605 samples, 167 were CHIKV-positive. Viral isolation was achieved for 20 samples; their phylogenetic analysis (E2 protein) revealed the presence of ECSA lineage and reinforced the phylogenetic relationship between ECSA and Indian Ocean lineages.

Conclusions: The genomic surveillance of CHIKV showed that only ECSA lineage circulated in Bahia since the 2014 outbreak.