TABLE. : Oligonucleotides designed in this study.
| Oligo | Sequence | Start | Stop |
|---|---|---|---|
| MAYV_FNF | 5’ CACGGACMTTTTGCCTTCA 3’ | 465 | 483 |
| MAYV_FNR | 5’ AGACTGCCACCTCTGCTKGAG 3’ | 524 | 504 |
| MAYV_FNP | 5’(VIC) ACAGATCAGACATGCAGG 3’ | 485 | 502 |
| OROV_FNF | 5’ TCCGGAGGCAGCATATGTG 3’ | 98 | 116 |
| OROV_FNR | 5’ ACAACACCAGCATTGAGCACTT 3’ | 160 | 139 |
| OROV_FNP | 5’(FAM) CATTTGAAGCTAGATACGG 3’ | 118 | 136 |
| MS2_IC_FNF | 5’ GCGCAGAATCGCAAATACA 3’ | 1494 | 1512 |
| MS2_IC_FNR | 5’ CAACAGTCTGGGTTGCCACTT 3’ | 1554 | 1534 |
| MS2_IC_FNP | 5’(NED) ATCAAAGTCGAGGTGCC 3’ | 1515 | 1531 |
Start/Stop numbers refers to the nucleotide position of Mayaro (MAYV) and Oropouche (OROV) S segment, and the Enterobacteria phage MS2 GenBank reference sequences (NC_003417.1, NC_005777.1, and NC_001417.2, respectively). All probes are TaqMan Minor Groove Binding (MGB) type with the fluorophores FAM, VIC, or NED as reporters and a non-fluorescent quencher. IDT DNA Technology synthesised all desalted primers used in this study with no further purification, whereas Applied Biosystems supplied the probes. The last digit in each oligo name was used to identify the forward (F) and reverse (R) primers, as well as the probes (P).