Evidence for current circulation of an ancient West Nile virus strain (NY99) in Brazil.

Introduction: In Brazil, West Nile virus (WNV) was first detected, in 2018, in horses with neurological disease.

Aim: We report the first case of WNV infection in a horse from Ceará state and the complete genome sequence of an isolate from Espírito Santo state. Both infections occurred in 2019.

Methods: WNV was isolated from the tissues of a horse with neurological signs in Espírito Santo and sequenced by MiSeq.

Results: Phylogenetic analysis revealed that the isolate belongs to lineage 1a, clustering with the NY99 strain, a strain that has not circulated in the USA since 2005.

Conclusions: Our findings reinforce the hypothesis that WNV has been silently circulating in Brazil for many years.