Table 3. List of selected targets and real-time PCR primer pairs designed for different viral species employed in this study.
| Species | Target | Forward primer (5’–3’) | Reverse primer (5’–3’) | Sequence numb. | Size (bp) |
|---|---|---|---|---|---|
| JPEV | NSP 5 | GGTACTACTGGGGCGAATGG | CCAAAAGGGGTGGTGTCAGT | 153 | 342 |
| SLEV | PreMP | ACAAGACTGACGCTCAAAGC | GGATTGCGCAAAACCCAGTT | 8 | 352 |
| TBEV | NSP 5 | ACAGCTAAACTTGCCTGGCT | ACGGTTTTTCCACTGCTCCA | 42 | 348 |
| USUV | NSP 5 | TCATGGAGCGCTTGGAAGTT | CAGGTCCGATATGGGTGGTC | 6 | 343 |
| WNV | NSP 1 | ACCAGAACTCGCCAACAACA | TCTCAAGGATTCCATCGCCC | 608 | 341 |
| CCHFV | Seg.a L | GCATCTCTGAAGTAACTGAAACAACA | GTTGAGATAGCACCGAGTTTCTTTAG | 41 | 154 |
| Seg. M | AGAAACAAGCTTATCAATTGAGGCAC | TGTCCTTTCTTCCAGCTTCATAATTG | 60 | 175 | |
| Seg. S | GATGAGATGAACAAGTGGTTTGAAGA | GTAGATGGAATCCTTTTGTGCATCAT | 65 | 159 | |
| SEOV | Seg. L | GTCTCACTTAGTACGAGTAAGGTTGA | AATTTTTGTCAGACATGCCTATACCG | 7 | 178 |
| Seg. M | CCTTGCAACAATTGATTCTTTTCAAT | ACAAGGATTCTCAGCCAAATTTTCAA | 18 | 160 | |
| Seg. S | GAAGAAATCCAGAGAGAAATCAGTGC | ATTTTTGATTGTATTGAAGCTGCGAC | 19 | 161 | |
| RVFV | Seg. L | ATGATGAATGACGGGTTTGATCATTT | AACCTCATACTTAGCGAGTTTAGTCA | 86 | 150 |
| Seg. M | GGCCCTTAGAGTTTTTAACTGTATCG | GGGCTCTCAATGAAAGAAAAGCTATT | 91 | 192 | |
| Seg. S | AACAATCATTTTCTTGGCATCCTTCT | ATAATGGACAACTATCAAGAGCTTGC | 141 | 180 |
aSeg., segment;
WNV, West Nile virus; SLEV, St. Louis encephalitis virus; JPEV, Japanese encephalitis virus; USUV, Usutu virus; TBEV, Tick-borne encephalitis virus; SEOV, Seoul virus; CCHFV, Crimean-Congo hemorrhagic fever virus; RVFV, Rift Valley fever virus.