Table 3.
Summary of results targeting MTC polymorphic loci
| Target Locus | Node #(s) in Fig. 2 | M. tuberculosis (n) | M. africanum WA-1 (n) | M. africanum WA-2 (n) | Other MTC (n) |
|---|---|---|---|---|---|
| RD loci | |||||
| RD12can/RD12 1 | 1, 17 | intact (18) | intact (20) | intact (9) | |
| 3'cfp32 | 1 | intact (18) | intact (20) | intact (9) | |
| TbD1 | 2 | deleted (18) | intact (20) | intact (9) | |
| pks15/1 | 3, 9 | 7-bp deletion (18) | intact (20) | 6-bp deletion (9) | |
| PPE55 2 | 4, 16 | intact (9) fail (9) |
intact (20) | intact (9) | |
| MiD3/RDRio 2 (IS1561' + PPE55) | 4, 16 | intact (9) fail (9) |
intact (20) | intact (9) | |
| RD9 | 6 | intact (18) | deleted (20) | deleted (9) | |
| RD713 3 | 7 | fail (18) | deleted (20) | fail (9) | |
| RD711 | 8 | intact (18) | deleted (20) | intact (9) | |
| RD7 3 | 9 | intact (18) | intact (20) | deleted (9) | |
| RD8 | 9 | intact (18) | intact (20) | deleted (9) | |
| RD10 | 9 | intact (18) | intact (20) | deleted (9) | |
| RD701 | 11 | intact (18) | intact (20) | deleted (9) | |
| RD702 | 11 | intact (18) | intact (20) | deleted (9) | |
| RD1das/RD1bcg 4 | 14, 19 | intact (18) | intact (20) | intact (9) | |
| RD13 | 17 | intact (18) | intact (20) | intact (9) | |
| RD4 | 18 | intact (18) | intact (20) | intact (9) | |
| SNP loci | |||||
| narGHJI -215 | 2 | C→T (18) | no Δ (20) | no Δ (9) | |
| katG463 | 3 | CTG→CGG (18) | no Δ (20) | no Δ (9) | |
| gyrA95 | 5 | no Δ (18) | no Δ (20) | no Δ (9) | |
| gyrB1450 | 6 | no Δ (18) | G→T (20) | G→T (9) | |
| TbD1197 | 7 | fail (18) | C→T (20) | no Δ (9) | |
| aroA285 | 7 | no Δ (18) | G→A (20) | no Δ (9) | |
| Rv1332523 | 7 | no Δ (27) | G→T (32) | no Δ (11) | no Δ (15) |
| katG203 | 9 | no Δ (18) | no Δ (20) | ACC→ACT (9) | |
| 3'cfp32311 | 9 | no Δ (18) | no Δ (20) | G→A (9) | |
| RD13174 | 9 | no Δ (18) | no Δ (20) | G→A (9) | |
| PPE552148 | 9 | no Δ (9) fail (9) |
no Δ (20) | A→G (9) | |
| PPE552154 | 9 | no Δ (9) fail (9) |
no Δ (20) | A→G (9) | |
| Rv15101129 | 10 | no Δ (18) | no Δ (20) | G→A (9) | |
| hsp65540 | 11 | no Δ (18) | no Δ (20) | C→G (9) | |
| nat751 | 11 | no Δ (63) | no Δ (32) | G→A (27) | no Δ (53) |
| rpoB1163 | 12 | no Δ (18) | no Δ (20) | C→T (9) | |
| rpoB1049 | 13 | no Δ (18) | no Δ (20) | no Δ (9) | |
| mmpL6551 | 15 | fail (18) | no Δ (20) | no Δ (9) | |
| Other targets | |||||
| cfp32 | intact (18) | intact (20) | intact (9) |
1,2,3,4 pairs of partially overlapping LSPs
WA, West African; Fail, no PCR amplification; bp, base pair; Δ, change