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Background  Flaviviruses are important pathogens for humans and animals (Dengue viruses, Yellow fever virus, Zika virus and West Nile virus). Culex flavivirus (CxFV) is an insect-specific virus of the genus  Flavivirus,  detected in a wide variety of mosquito species.    Objective  To detect Flavivirus in mosquitoes of a tropical region of the Colombian Caribbean.    Methods  In 2014, an entomological surveillance of arboviruses was conducted in the department of Cordoba area of the Caribbean, Colombia. A total of 8270 mosquitoes were captured as follow:  Mansonia  ( n  = 3271/39.5%),  Culex  ( n  = 2668/32.26%),  Anopheles  ( n  = 840/10.15%),  Aedeomyia  ( n  = 411/4.9%),  Psorophora  ( n  = 397/4.8%),  Coquilletidia  ( n  = 369/4.46%),  Uranotaenia  ( n  = 261/3.15%) and  Aedes  ( n  = 53/0.6%). All mosquito species were collected in dry tropical forest of the Caribbean area. Universal primers for NS5 gene (958 pb), RT-PCR for flavivirus and sequencing were used for molecular identification of viruses detected.    Results  Two pools belonging to  Culex coronator  were positive for flavivirus RNA sequence by RT-PCR. The sequences of the PCR amplicons, matched that of the Culex flaviviruses, CxFv COL PM_149 (GenBank: KR014201) and CxFv COL PM_212 (GenBank: KT307717). Phylogenetic analysis of the NS5 protein sequences of the Culex flaviviruses sequences with those of reference sequences available in GenBank indicated viruses of Genotype II, closely related to the Brazilian strain, BR_SJRP_01_ (GenBank: KT726939), from  Culex  sp. The alignment of Culex flavivirus sequences CxFv COL_ PM 212 and CxFv COL_ PM 149 with sequences of strains detected in different geographical regions grouped the strains in a Latin American clade reported in Brazil, Argentina and Mexico.    Conclusions  The present work illustrated that CxFV was circulating among vectors of human pathogenic arboviruses in Colombia, but the impact of CxFV on other flaviviruses which are endemic in the study area still remains to be explored.    Electronic supplementary material  The online version of this article (10.1186/s12985-018-1108-2) contains supplementary material, which is available to authorized users.

First report of Culex flavivirus infection from Culex coronator (Diptera: Culicidae), Colombia