Table 2.
Specific L4 sub-lineages primers used in the study.
| MTBC Sub-lineage* | SNP position† | Nucleotide change‡ | Gene | Primers 5′-3′ | Amplicon size | Reference |
|---|---|---|---|---|---|---|
| L4.1.1 | 3798451§ | C/G | Rv3383c | F-ATCGACTCAATGGCCCGATG | 112 bp | This study |
| R-TGACTCTGGATGCGGTTTT | ||||||
| L4.1.2 | 4323348§ | C/T | Rv3848/3849 | F-AAATCCGTTCGTCGTGTGGA | 82 bp | This study |
| R-CTGACGTTGTGAGGGGTCAA | ||||||
| L4.1.3 | 4409231 | T/G | Rv3921c | F-GACCGCCTCCTGCTTTTTG | 53 bp | This study |
| R- ACGTCTTCGGCATGATCGAA | ||||||
| L4.2 | 2942377 | C/T | Rv2614c | F-GAGTAGTCCTCCAGTTCGCG | 85 bp | This study |
| R-TCAGCTTCCCCGACGAAATC | ||||||
| L4.3 | 1480024§ | G/T | Rv1318c | F-CAGGCCAGGATCCACATCAG | 100 bp | This study |
| R-TGCTGCTCAATCTCACTCGG | ||||||
| L4.4 | 4307886 | G/A | Rv3834c | F-AAGGTGGTGCAGTTCGAC | 69 bp | This study |
| R-ACTGCGAGGCGTGGATTC | ||||||
| L4.5 | 2789341§ | A/C | Rv2483c | F-GGAGGCCTCACCATCCTTG | 81 bp | This study |
| R-ACGAAGGCGGCTACAAAGAA | ||||||
| L4.6.1 | 435708 | G/A | Rv0357c | F-CAAAGATCCCGCTGGGTCAT | 58 bp | This study |
| R-GATATGAGATCGACGGCCGG | ||||||
| L4.6.2 | 3191099§ | C/A | Rv2881c | F-CATCATGCAGAACACCCATC | 72 bp | This study |
| R-CCCATTGTTCTGCTCTTTCG | ||||||
| L4.10 | 1692141§ | C/A | Rv1501 | F-GCTCGGTGTTCTTCGACTCA | 107 bp | This study |
| R-TGGCCGTTTCAGATAGCACA |
*Nomenclature proposed by Stucki et al.6.
†Genomic position on the H37Rv reference genome (NCBI, NC_000962.3).
‡Allelic change in the reference genome.
§Mutation previously described by Stucki et al.6.