The complex pattern of genetic associations of leprosy with HLA class I and class II alleles can be reduced to four amino acid positions

Leprosy is a chronic disease caused byMycobacterium leprae. Worldwide, more than 200,000 new patients are affected by leprosy annually, making it the second most common mycobacterial disease after tuberculosis. The MHC/HLA region has been consistently identified as carrying major leprosy susceptibility variants in different populations at times with inconsistent results. To establish the unambiguous molecular identity of classical HLA class I and class II leprosy susceptibility factors, we applied next-generation sequencing to genotype with high-resolution 11 HLA class I and class II genes in 1,155 individuals from a Vietnamese leprosy case-control sample. HLA alleles belonging to an extended haplotype fromHLA-AtoHLA-DPB1were associated with risk to leprosy. This susceptibility signal could be reduced to theHLA-DRB1*10:01 similar to HLA-DQA1*01:05alleles which were in complete linkage disequilibrium (LD). In addition, haplotypes containingHLA-DRB3 similar to HLA-DRB1*12:02andHLA-C*07:06 similar to HLA-B*44:03 similar to HLA-DRB1*07:01alleles were found as two independent protective factors for leprosy. Moreover, we replicated the previously associatedHLA-DRB1*15:01as leprosy risk factor andHLA-DRB1*04:05 similar to HLA-DQA1*03:03as protective alleles. When we narrowed the analysis to the single amino acid level, we found that the associations of the HLA alleles were largely captured by four independent amino acids at HLA-DR beta 1 positions 57 (D) and 13 (F), HLA-B position 63 (E) and HLA-A position 19 (K). Hence, analyses at the amino acid level circumvented the ambiguity caused by strong LD of leprosy susceptibility HLA alleles and identified four distinct leprosy susceptibility factors.