TABLE 2.
Locus designations and primer sequences used in this study for the hypervariable loci
| Markera | Alias | Consensus panel | Primer pair, 5′–3′ (dye) | Reference | Amplicon size (bp) in H37Rv | Repeat no. × length (bp) in H37Rv |
|---|---|---|---|---|---|---|
| 1982 | QUB-18 | Included | CCGGAATCTGCAATGGCGGCAAATTAAAAG | 2 | 620 | 5 × 78 |
| TGATCTGACTCTGCCGCCGCTGCAAATA (NED) | ||||||
| 3232 | QUB-3232 | Included | CACTAGTTGTTGCGGCGATGG | 41 | 421 | 3 × 56b |
| AAGGGCGGCATTGTGTTC (FAM) | ||||||
| 3820 | Included | ACCTTCATCCTTGGCGAC (NED) | 42 | 444 | 3 × 57 | |
| TGCGCGGTGAATGAGACG | ||||||
| 4120 | Included | GTTCACCGGAGCCAACC (FAM) | 42 | 447 | 2 × 57 | |
| GAGGTGGTTTCGTGGTCG | ||||||
| 2163a | QUB-11a | Excluded | TGTTGAAGAAGCCCGAAGAC (PET) | This study | 451 | 3 × 69 |
| CCGTTTAACGTCGCTGGTAT | ||||||
| 3155 | QUB-15 | Excluded | AGGGGTTCTCGGTCACCC (VIC) | 43 | 252 | 3 × 54 + 1 × 45c |
| TACATTCGCGGCCAAAGG | ||||||
| 3336 | QUB-3636 | Excluded | GATCGGGTGCAGTGGTTTCAGGTG | This study | 571 | 5 × 59 |
| GGGCGGCCAGCGGTGTC (VIC) |
a
Markers are coded by conventional numbers indicating their position (in kbp) on the M. tuberculosis H37Rv chromosome.
b
Additional incomplete repeat unit of 48 bp not taken into consideration for allele reporting, by convention.
c
Repeat units of 54 and 45 bp are jointly considered for allele reporting (i.e., 3 × 54 + 1 × 45 = allele 4), by convention.