The RV144 HIV vaccine trial in Thai

The RV144 HIV vaccine trial in Thailand elicited two different antibody responses to the
envelope of HIV-1, which correlated significantly with the risk of HIV-1 acquisition. HLA class II
molecules are essential in antigen presentation to CD4 T cells for activation of B cells to
produce antibodies. We genotyped the classical HLA-DRB1, DQB1 and DPB1 genes in 450
individuals from the placebo arm of the RV144 study to determine the background allele and
haplotype frequencies of these genes in this cohort. Understanding the interaction of HLA class
II genes with the immune correlates in RV144 could shed light on mechanisms that mediate
humoral responses and impact vaccine efficacy.
High-resolution 4 and 6-digit class II HLA typing data was generated using sequencing
based methods. The observed diversity for the HLA loci was 33 HLA-DRB1, 15 HLA-DQB1, and
26 HLA-DPB1 alleles. Common alleles with frequencies greater than 10% were DRB1*07:01,
DRB1*09:01, DRB1*12:02, DRB1*15:02, DQB1*02:01, DQB1*03:01, DQB1*03:03,
DQB1*05:01, DQB1*05:02, DPB1*04:01:01, DPB1*05:01:01 and DPB1*13:01:01. We identified
28 rare alleles with frequencies of less than 1% in the Thai individuals. Ambiguity for HLADPB1*
28:01 in exon 2 was resolved to HLA-DPB1*296:01 by sequencing all exons. The two
and three-loci haplotypes were reported for all three class II genes.
This is the first comprehensive report of allele and haplotype frequencies of all three
HLA class II genes from a Thai population. A high-resolution genotyping method like nextgeneration
sequencing avoids missing rare alleles and resolves ambiguous calls. The HLA
class II genotyping data generated in this study will be beneficial not only for future disease
association/vaccine efficacy studies related to the RV144 study, but also for similar studies in
other diseases in the Thai population, as well as population genetics and transplantation
studies.