Table 2 Primers and probes used in this study
From: High level of genomic divergence in orf-I p12 and hbz genes of HTLV-1 subtype-C in Central Australia
ODP ID | Sequence (5′ → 3′) | Purpose |
|---|---|---|
HTLV-1c PVL quantification by ddPCR | ||
 3083 | CAAATGAAGGACCTACAGGC | Forward primer for HTLV-1c gag |
 3084 | TATCTAGCTGCTGGTGATGG | Reverse primer for HTLV-1c gag |
 3321 | 6FAM-ACCATCCGGCTTGCAGT-MGBNFQ | Probe for HTLV-1c gag |
 3085 | TCCAGGCCTTATTTGGACAT | Forward primer for HTLV-1c tax |
 3086 | CGTGTGAGAGTAGGACTGAG | Reverse primer for HTLV-1c tax |
 3318 | 6FAM-CATGATTTCCGGGCCTTGC-MGBNFQ | Probe for HTLV-1c tax |
Unrearranged T-cell receptor beta (UTCRβ) locus quantification by ddPCR | ||
 3190 | TGTACAAAGCTGTAACATTGTGGGGAC | Forward primer for UTCRβ |
 3191 | AACCAAATTGCATTAAGACCTGTGACC | Reverse primer for UTCRβ |
 3191a | 6FAM-ACAATGATTCAACTCTACGGGAAACC-MGBNFQ | Probe for UTCRβ |
Primer walking strategy, step 1—outer PCR | ||
 3100 | ATAAACTTAAGTGATACTGACCATGGGCCCCAAATAC | Forward primer for fragment A |
 3160 | CTATCTAGCTGCTGGTGATGGAGGG | Reverse primer for fragment A |
 3161 | CCCTCCATCACCAGCAGCTAGATAG | Forward primer for fragment B |
 3162 | GAGTCTAAAAATATGTTGAGACAGTGCC | Reverse primer for fragment B |
 3163 | GGCACTGTCTCAACATATTTTTAGACTC | Forward primer for fragment C |
 3164 | ATAAAGGATCCACTGGGCAGAATTGGCGC | Reverse primer for fragment C |
 3165 | ATAAAGGATCCCGTGGAGGCTCCTCAAGC | Forward primer for fragment D |
 3141 | GGAAAAGGGTGGTGGGTAAACAGCC | Reverse primer for fragment D |
 3166 | GGCTGTTTACCCACCACCCTTTTCC | Forward primer for fragment E |
 3101 | ATAAACTTAAGTGTGTTCTATGTCTCTCTCCTGGAGAGAGG | Reverse primer for fragment E |
Primer walking strategy, step 2—inner PCR | ||
 3040 | TGTGTTCTATGTCTCTCTCCTGGAGAGAGGTATAGAATG | Reverse primer for fragment A1 Paired with ODP 3100 |
 3207 | TTCCCTTTCATTCACGTCTGACTGC | Forward primer for fragment A2 Paired with ODP 3160 |
 3184 | TTAGAGAATTAGTGGCCCGCAGG | Reverse primer for fragment B1 Paired with ODP 3161 |
 2934 | CAATGGAACCTGGCG | Forward primer for fragment B2 Paired with ODP 3162 |
 3189 | AGAGTAATGGGGGTATCTGGTGC | Reverse primer for fragment D1 Paired with ODP 3165 |
 2938 | TCCTTGCAGGACCATGC | Forward primer for fragment D2 Paired with ODP 3024 |
 3024 | TCTCCATACACGTAGACT | Reverse primer for fragment D2 Paired with ODP 2938 |
 3023 | CACACCGTCAAGCACAGATT | Forward primer for fragment D3 Paired with ODP 3141 |
 2944 | GCGTGCCATGAAAAG | Reverse primer for fragment E1 Paired with ODP 2944 |
 3039 | TGATACTGACCATGGGCCCCAAATACCTTCC | Forward primer for fragment E2 Paired with ODP 3101 |