Revisiting the emergence of the Chikungunya virus in Alagoas, Northeast of Brazil.

Chikungunya virus (CHIKV), an Alphavirus, emerged in the Americas in 2013 and was first documented in Brazil in September 2014, in the states of Pará and Bahia. Although Alagoas state officially reported its first case in late 2015, this study investigated potential earlier unreported cases by analyzing samples from a 2013-2014 Orthoflavivirus serological survey. We screened sera from patients with acute febrile illness, initially suspected of dengue but negative in molecular tests for the genus Orthoflavivirus, using ELISA (IgM/IgG), viral isolation, PCR, and next-generation sequencing. Two samples collected in June and August 2014 tested positive for anti-CHIKV IgM, and four additional samples collected between June and September 2014 tested positive for anti-CHIKV IgG antibodies. From one sample IgM-positive (630H) collected in August 2014, we isolated and sequenced a nearly complete genome (95.53% coverage, 2714× depth) classified as the East-Central-South-African (ECSA) genotype. Phylogenetic analyses revealed that the Alagoas-2014 genome formed a distinct, well-supported clade separate from the Bahia 2014 lineage. Temporal inference dated this lineage's origin to October 2013 (90% CI: April 2013-March 2014), suggesting a new introduction of ECSA into Alagoas. This genomic evidence, along with serological data, confirms the undetected early circulation of CHIKV in Alagoas and suggests a possible introduction of ECSA in Brazil in 2014, distinct from the well-documented introduction in Bahia.