Persistence of chikungunya ECSA genotype and local outbreak in an upper medium class neighborhood in Northeast Brazil
Goes De Jesus J., Da Luz Wallau G., Lima Maia M., Xavier J., Oliveira Lima MA., Fonseca V., De Abreu AS., De Oliveira Tosta SF., Do Amaral HR., Lima IAB., Silva PV., Dos Santos DC., De Oliveira AS., De Souza SC., Falcao MB., Cerqueira E., Machado LC., Sobral MC., Rezende TMT., Pereira MR., Pereira FM., Maia ZPG., De Oliveira Francça RF., De Abreu AL., De Albuquerque E Melo CFC., Faria NR., Da Cunha RV., Giovanetti M., Alcantara LC.
Copyright © 2020 Goes de Jesus et al. 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 synonymous, 21 are non-synonymous and one generated a stop codon. Although those mutations are not related to the increase of virus replication and/or infectivity, some SNPs were found in non-structural proteins which may have an effect on viral evasion from the mammal immunological system. These findings reinforce the needing of further studies on those variants and of continued genomic surveillance strategies to track viral adaptations and to monitor CHIKV epidemics for improved public health control.