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Background  Culex Flavivirus (CxFV) is an insect-specific virus that is widely distributed and primarily infects mosquito species from the genus  Culex . Its hosts include  Culex tritaeniorhynchus ,  Culex quinquefasciatus , and  Anopheles sinensis  mosquitoes. Since its original identification, CxFV has been reported in several countries. Despite the increasing number of reports on CxFV, little is known about its genomic characteristics. It is unclear whether the phylogenetic relationships between the strains are influenced by host species and geographic location.    Results  We characterized the Brazilian CxFV strain and performed a comprehensive genetic and phylogenetic characterization of CxFV based on all ORF sequences described so far. Our results revealed that the Brazilian strain is in a monophyletic clade with the Mexican strain. Overall, selective pressure indicates that the ORF is undergoing purifying selection.    Conclusions  The phylogenetic analysis revealed a strong association between climate and CxFV ancestry. Also, based on phylogeny and the genetic distance between the main branches of the tree, we propose the classification of the available sequences into two different genotypes. We also suggest the existence of two different subtypes within Genotype 1.    Electronic supplementary material  The online version of this article (doi:10.1186/s12985-016-0614-3) contains supplementary material, which is available to authorized users.

Genome sequencing and genetic characterization of Culex Flavirirus (CxFV) provides new information about its genotypes