4.6 Article

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

Journal

VIRUSES-BASEL
Volume 14, Issue 10, Pages -

Publisher

MDPI
DOI: 10.3390/v14102311

Keywords

CHIKV; ECSA; Brazil; Arbovirus; Aedes spp; phylogenetic analysis

Categories

Funding

  1. Rede Corona-omica BR MCTI/FINEP [FINEP = 01.20.0029.000462/20, CNPq = 404096/2020-4]
  2. Fundacao de Apoio a Pesquisa do Distrito Federal (FAP-DF) [193001532/2016]
  3. National Council for Scientific and Technological Development-CNPq [443215/2019-7]

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This study investigates the genomic epidemiology of the CHIKV virus in Tocantins state, Brazil, and finds that the virus belongs to the ECSA lineage and is closely related to outbreaks in Northeast and Southeast Brazil. The study identifies several frequent non-synonymous mutations in the virus genome, indicating local transmission in the state. The findings highlight the importance of continued genomic surveillance for predicting new infections and improving public health services.
The chikungunya virus (CHIKV) is a mosquito-borne virus of the family Togaviridae transmitted to humans by Aedes spp. mosquitoes. In Brazil, imported cases have been reported since June 2014 through two independent introductions, one caused by Asian Lineage in Oiapoque, Amapa state, North Region, and another caused by East/Central/South African (ECSA) in Feira de Santana, Bahia state, Northeast Region. Moreover, there is still limited information about the genomic epidemiology of the CHIKV from surveillance studies. The Tocantins state, located in Northern Brazil, reported an increase in the number of CHIKV cases at the end of 2021 and the beginning of 2022. Thus, to better understand the dispersion dynamics of this viral pathogen in the state, we generated 27 near-complete CHIKV genome sequences from four cities, obtained from clinical samples. Our results showed that the newly CHIKV genomes from Tocantins belonged to the ECSA lineage. Phylogenetic reconstruction revealed that Tocantins' strains formed a single well-supported clade, which appear to be closely related to isolates from the Rio Grande do Norte state (Northeast Brazil) and the Rio de Janeiro state (Southeast Brazil), that experienced an explosive ECSA epidemic between 2016-2019. Mutation analyses showed eleven frequent non-synonymous mutations in the structural and non-structural proteins, indicating the autochthonous transmission of the CHIKV in the state. None of the genomes recovered within the Tocantins samples carry the A226V mutation in the E1 protein associated with increased transmission in A. albopictus. The study presented here highlights the importance of continued genomic surveillance to provide information not only on recording mutations along the viral genome but as a molecular surveillance tool to trace virus spread within the country, to predict events of likely occurrence of new infections, and, as such, contribute to an improved public health service.

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