TABLE 1.

List of primers used in this study.

Primer name	Target	Purpose	Amplicon size (bp)	Primer sequence (5′–3′)	Nucleic acid modification between strains	References
RLEP-F	RLEP	Detection of M. leprae by	450	TGAGGCTTCGTGTGCTTTGC	–	Singh et al., 2015
RLEP-R	RLEP	PCR		ATCTGCGCTAGA AGGTTGCC	–
RLEPq-F	RLEP	Detection of M. leprae by	70	GCAGTATCGTGTTAGTGAA	–	Truman et al., 2008
RLEPq-R	RLEP	quantitative PCR		CGCTAGAAGGTTGCCGTATG	–
RLEPq-P	RLEP			FAM-TCGATGATCCGGCCGTCGGCG QSY	–
LPM244-F	hemN	Detection of	244	GTTCCTCCACCGACAAACAC	–	Singh et al., 2015
LPM244-R		M. lepromatosis		TTCGTGAGGTACCGGTGAAA	–
rpoB-For	rpoB	Amplification of the drug	255	CTGATCAATATCCGTCCGGT	–	WHO SEARO/Department of Control of Neglected Tropical Diseases, 2017
rpoB-Rev		resistance-determining region of rpoB		CGACAATGAACCGATCAGAC	–
folP1-For	folP1	Amplification of the drug	254	CTTGATCCTGACGATGCTGT	–
folp1-Rev		resistance-determining region of folP1		CCACCAGACACATCGTTGAC	–
gyrA-For	gyrA	Amplification of the drug	225	ATGGTCTCAAACCGGTACATC	–
gyrA-Rev		resistance-determining region of gyrA		TACCCGGCGAACCGAAATTG	–
SNP-2921694-F	ml2446	Specific to 1D-Malagasy	169	TGTATGAACGCTGGGCAGTA	A1015G	This study
SNP-2921694-R		genotype		TCAACCGGGTCACCATAGAT
SNP-3016895-F	ml2535	Specific to 1D genotype	199	GAGCCACTATTTCCCGACAA	C3541A	This study
SNP-3016895-R		outside Madagascar		CGTCGTCGATGAGCAAGTAA