Persistence of chikungunya ECSA genotype and local outbreak in an upper medium class neighborhood in Northeast Brazil

Abstract

The chikungunya East/Central/South/Africa virus lineage (CHIKV-ECSA) was first detected in Brazil in the municipality of Feira de Santana (FS) by mid 2014. Following that, a large number of CHIKV cases have been notified in FS, which is the second-most populous city in Bahia state, northeastern Brazil, and plays an important role on the spread to other Brazilian states due to climate conditions and the abundance of competent vectors. To better understand CHIKV dynamics in Bahia state, we generated 5 complete genome sequences from a local outbreak raised in Serraria Brasil, a neighbourhood in FS, by next-generation sequencing using Illumina approach. Phylogenetic reconstructions revealed that the new FS genomes belongs to the ECSA genotype and falls within a single strongly supported monophyletic clade that includes other older CHIKV sequences from the same location, suggesting the persistence of the virus during distinct epidemic seasons. We also performed minor variants analysis and found a small number of SNPs per sample (b_29L and e_45SR = 16 SNPs, c_29SR = 29 and d_45PL and f_45FL = 21 SNPs). Out of the 93 SNPs found, 71 are

Genomic Epidemiology Reveals the Circulation of the Chikungunya Virus East/Central/South African Lineage in Tocantins State, North Brazil

“…In Brazil, the local transmission of the Asian lineage was detected for the first time in September 2014 in the Oiapoque city, Amapá state, North Region. Seven days later, a new cluster of CHIKV infections was notified in the city of Feira de Santana, Bahia state, Northeast Region [ 12 , 13 , 14 , 15 ]. Since then, the disease has spread across the country, posing a serious threat to public health.…”

Phylogenetic Characterization of Arboviruses in Patients Suffering from Acute Fever in Rondônia, Brazil

“…To highlight the importance of investigating these variants, the ECSA genotype (East/Central/South African), when compared to the African genotype S-27 (S-27) in mice, caused a high and acute fatality, with a higher viral load in the central nervous system and peripheral organs [22]. This genotype has endured in northeastern Brazil, since its first detection in the country in 2014 [23], which shows concern about its circulation and its possible consequences on the population's health.…”

Chikungunya virus transmission in the Southernmost state of Brazil was characterized by self-limited cases (2017–2019) and a larger 2021 outbreak

“…However, after the first years of expansion, these genotypes have been undergoing distinct transmission dynamics. While the AC genotype remained mostly restricted to the North region (13), the ECSA genotype is spreading widely and has been detected in all Brazilian states (9,12,14,15,17,17–19). A recent study showed that the most affected region of Brazil was the Northeast (16), whereas limited CHIKF cases had been detected in the South region (20,43).…”

“…Early studies characterizing these events suggested that both lineages would spread and cause outbreaks country-wide, with a higher transmission potential in the tropical region (8). This hypothesis was later corroborated with several Brazilian states in the North, Northeast, Southeast and Central-West regions experiencing large CHIKV outbreaks; whereas the South region experienced lower CHIKV incidence (12)(13)(14)(15)(16)(17)(18)(19).…”