Genetic characterization of the complete genome of a strain of Chikungunya virus circulating in Brazil: a strategy for the surveillance and control of Arboviral diseases with epidemic potential in Latin America.

Chikungunya virus (CHIKV) is a positive-sense single-stranded RNA virus that belongs to the Alphavirus genus of the Togaviridae family. It is mainly transmitted by mosquitoes Aedes aegypti and albopictus. Its genome encodes four non-structural proteins (NSP 1-4 encoded at the 5 end) and three structural proteins (C, E1 and E2 structural proteins encoded at the 3 end). Four lineages of this virus have been identified, namely the lineages from 1) West Africa, 2) East, Central and South Africa (ECSA), 3) Asia (AL) and 4) Indian Ocean (IOL). CHIKV is an endemic arbovirus circulating in 51 countries in the Americas. The clinical manifestations attributed to it are: high fever, rash, myalgia and episodes of arthralgia, which consequently lead to chronic pain and disability, especially in the joints. Whole genome sequencing of the Chikungunya virus is essential to understand its biology, evolution and spread, and to develop effective prevention, diagnosis and treatment strategies. This information is essential to combat the disease and minimize its impact on public health. For these reasons, the complete genome of the Chikungunya virus BR33, identified in the northeastern city of Recife, in the state of Pernambuco, Brazil, was sequenced. The genome has a size of 11,601 nucleotides and fragments that code for two polyproteins. A phylogenic analysis was performed indicating that the recent Brazilian strain of CHIKV belongs to the East, Central and Southern Africa (ECSA) lineage. This phylogenetic identification is important because this particular genotype has been associated with greater damage and clinical severity, in addition to the fact that this ECSA lineage has a wide range of genomic diversity. Until 2016, CHIKV was directly associated with travel and transmission was limited. Subsequently, in the State of Pernambuco, Brazil, the introduction of a new ECSA lineage was identified, which corresponds to the one identified in this study and which generated the largest outbreak. New CHIKV outbreaks are very likely in the near future due to the abundance of competent vectors in Brazil and a susceptible population, exposing more than 11 million inhabitants to an increasing risk of infection.