Table 8.

Concordance of PCR-RFLP and real-time PCR-HRM methods for M. leprae SNP typing of clinical isolates

Sample	Sample type	PCR-RFLPa		SNP type	HRM clusterb
		Locus 2/CviKI	Locus 3/BstUI		Locus 1	Locus 2	Locus 3
NP101	Clinical	—	—	1	1	2	2
NP103	Clinical	—	—	1	1	2	2
NP108	Clinical	—	—	1	1	2	2
NP109	Clinical	—	—	1	1	2	2
NP110	Clinical	—	—	1	1	2	2
NP111	Clinical	—	—	1	1	2	2
NP112	Clinical	—	—	1	1	2	2
NP114	Clinical	—	—	1	1	2	2
NP116	Clinical	—	—	1	1	2	2
NP117	Clinical	—	—	1	1	2	2
NP118	Clinical	—	—	1	1	2	2
NP119	Clinical	—	—	1	1	2	2
NP120	Clinical	—	—	1	1	2	2
NP123	Clinical	—	—	1	1	2	2
NP106	Clinical	—	—	1	Vc/1	2	2
NP113	Clinical	—	—	1	Vc/1	2	2
NP102	Clinical	+	—	2	1	1	2
NP104	Clinical	+	—	2	1	1	2
NP115	Clinical	+	—	2	1	1	2
NP122	Clinical	+	—	2	1	1	2
NP124	Clinical	+	—	2	1	1	2
NP105	Clinical	+	—	2	1	1	2
NP121	Clinical	+	—	2	1	1	2
NP125	Clinical	NDd	—	2	1	Vc/1	2
NP107	Clinical	ND	—	1	1	2	2
NHDP63	ADML	+	+	3	1	1	1
Thai53	ADML	—	+	1	1	2	2
BR4923	ADML	+	+	4	2	1	1

^aThe PCR-RFLP assay was performed as previously described (31).

^bThe NHDP63 allele is assigned to cluster 1 and the alternative allele to cluster 2.

^cV, HRM automatically grouped the three strains NP106, NP113, and 125 into a different cluster (variant). When the melting curves were manually examined, NP113 and NP125 were in the same cluster as NHDP63, while NP106 appeared to belong to a different cluster. Locus 1 amplicons of NP106 was sequenced, and SNP allele C was same as that of the NHDP63 and TN strains.

^dND, not determined due to small amount of amplicon.