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 from horses with neurological disease. Aim: Here we present the first reported case in Ceara state and complete genome sequence from an isolated in Espirito Santo state from 2019. Methods: The virus was isolated from a horse that died with neurological signs in Espirito Santo and was sequenced by MiSeq. Results: Phylogenetic analysis reveals that this isolate belongs to lineage 1a, clustering with NY99 strain, that disappeared from the USA since 2005. Conclusions: Our findings reinforce the hypothesis that WNV has been silently circulating in Brazil for many years.