TABLE 1.
Primer sequence and repeat unit size in M. tuberculosis H37Rv of the VNTR loci used in this study
| VNTR locus | VNTR locus alias | VNTR locus convention (28) | PCR primer sequence (5′-3′) | Repeat unit size (bp) × no. in H37Rva |
|---|---|---|---|---|
| ETR-A | VNTR 2165 | CGA AGC CTG GGG TGC CCG CGA TTT | (75 × 3) + 23 | |
| AAA TCG GTC CCA TCA CCT TCT TAT | ||||
| ETR-B | VNTR 2461 | GCG AAC ACC AGG ACA GCA TCA TG | (57 × 3) + 8 | |
| GGC ATG CCG GTG ATC GAG TGG | ||||
| ETR-C | VNTR 0577 | GTG AGT CGC TGC AGA ACC TGC AG | (58 × 4) − 21 | |
| GGC GTC TTG ACC TCC ACG AGT G | ||||
| ETR-D | MIRU4 | VNTR 0580 | CAG GTC ACA ACG AGA GGA AGA GC | (77 × 3) + 7 |
| GCG GAT CGG CCA GCG ACT CCT C | ||||
| ETR-Eb | MIRU31 | VNTR 3192 | CTT CGG CGT CGA AGA GAG CCT C | (53 × 3) − 4 |
| CGG AAC GCT GGT CAC CAC CTA AG | ||||
| MIRU10 | VNTR 0960 | GTT CTT GAC CAA CTG CAG TCG TCC | 53 × 3 | |
| GCC ACC TTG GTG ATC AGC TAC CT | ||||
| MIRU16 | VNTR 1644 | TCG GTG ATC GGG TCC AGT CCA AGT A | 53 × 2 | |
| CCC GTC GTG CAG CCC TGG TAC | ||||
| MIRU20c | VNTR 2059 | TCG GAG AGA TGC CCT TCG AGT TAG | 77 × 2 | |
| GGA GAC CGC GAC CAG GTA CTT GTA | ||||
| MIRU26 | VNTR 2996 | TAG GTC TAC CGT CGA AAT CTG TGA C | 51 × 3 | |
| CAT AGG CGA CCA GGC GAA TAG | ||||
| MIRU31b | ETR-E | VNTR 3192 | ACT GAT TGG CTT CAT ACG GCT TTA | 53 × 3 |
| GTG CCG ACG TGG TCT TGA T | ||||
| MIRU39 | VNTR 4348 | CGC ATC GAC AAA CTG GAG CCA AAC | 53 × 2 | |
| CGG AAA CGT CTA CGC CCC ACA CAT | ||||
| MIRU40 | VNTR 0802 | GGG TTG CTG GAT GAC AAC GTG T | 54 × 1 | |
| GGG TGA TCT CGG CGA AAT CAG ATA | ||||
| QUB11a | VNTR 2163a | TTC AGG GGG GAT CCG GGA | (69 × 2) + 8 | |
| CCC ATC CCG CTT AGC ACA TTC GTA | ||||
| QUB11b | VNTR 2163b | CGT AAG GGG GAT GCG GGA AAT AGG | (69 × 5) + 9 | |
| CGA AGT GAA TGG TGG CAT | ||||
| QUB26 | VNTR 4052 | GGC CAG GTC CTT CCC GAT | (111 × 5) + 24 | |
| AAC GCT CAG CTG TCG GAT | ||||
| QUB1895 | VNTR 1895 | GGT GCA CGG CCT CGG CTC C | (57 × 4) + 11 | |
| AAG CCC CGC CGC CAA TCA A | ||||
| QUB3232c | VNTR 3232 | CAG ACC CGG CGT CAT CAA C | (56 × 3) + 50 | |
| CCA AGG GCG GCA TTG TGT T | ||||
| QUB3336c | VNTR 3336 | ATC CCC GCG GTA CCC ATC | 59 × 5 | |
| GCC AGC GGT GTC GAC TAT CC |
a
Some loci have several complete repeats and one partial repeat. For example, the ETR-A locus contains three complete 75-bp repeats followed by an additional 23 bp of repetitive sequence.
b
Note that ETR-E and MIRU31 designate the same locus.
c
The amplification of MIRU20, QUB3232, and QUB3336 was not successful by using the protocol of Frothingham and Meeker-O'Connell (8).