SNP7614 and indel_17915 allowed for rapid and unambiguous identification of M. leprae strains containing SNP type 3I. Type 3I SNPs can be further subdivided into types 3I-1 and 3I-2 on the basis of SNP1527056 and four other SNPs (not shown). Samples with two copies of indel_17915 are classified into major SNP types 1, 2, 3, and 4 (as previously described4) and then further subtyped as a single letter from A though P, as shown, on the basis of the listed SNPs (which are representative of a panel of 84 SNPs22). Further high-resolution classification was then based on analysis of 10 variable-number tandem repeats (VNTRs).