The extracted RNA was converted to cDNA using the Revert Aid RT kit (Thermo Fisher Scientific,Waltham, Massachusetts, US ) according to manufacturer’s instructions. PCR was performed using genus specific primers targeting the non-structural protein 5 (NS5) of the Flavivirus genome [51]. Briefly, conventional PCR was performed using the Phusion Green Hot Start II High-Fidelity PCR Master Mix (Thermo Fisher Scientific). For each reaction, 2 µL of template was used together with 10 µL of the 2x Phusion mix, 1.25 µL of both forward (FU 1; 5′- TAC AAC ATG ATG GGA AAG AGA GAG AA-3′) and reverse primers (CFD2; 5′- GTG TCC CAG CCG GCG GTG TCA TCA GC-3′) (10 pmol), 0.6 µL of DMSO and 4.9 µL of nuclease free water, up to a total reaction volume of 20 µL. Conditions for reactions were 98°C for 30 s for initial denaturation. Further, amplification was performed using 35 cycles of: 98°C for 7 s, 60°C for 15 s and 72°C for 20 s. Final extension was performed at 72°C for 7 min. The PCR products were analysed by gel electrophoresis using 3% agarose in 1x TAE with GelRed (Biotium Inc. Hayward, CA, US) and later purified with ExoSAP-IT kit (Thermo Fisher Scientific) and sent to Eurofin Genomics (Germany) for Sanger sequencing. Sequences were then aligned to previously identified Flavivirus strains in GenBank using the Basic Local Alignment Search Tool (BLAST) provided by the National Center for Biotechnology Information.