O4-17. Genome wide association studies to characterize the HIV-1 positive Elite Controller (EC) cohort in Sweden
Sara Svensson Akusjärvi , Anoop T Ambikan , Maike Sperk , Wang Zhang [1,2], Kajsa Noyan , Anders Sonnerborg [1,3], Ujjwal Neogi 
Affiliates:  Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Sweden.  Science for Life Laboratory, Division of Proteomics and Nanobiotechnology, KTH Royal Institute of Technology, Stockholm, Sweden.  Department of Medicine Huddinge, Unit of Infectious Diseases, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
Several genome-wide association studies (GWAS) have tried to identify the background for HIV control, multiple independent polymorphisms have been identified within the HLA and CCR5-CCR2 locus that together explain ~25% of the observed variability in viral load. In this study, we aimed to define the host genetic characteristics coupled to clinical phenotypes in a well-defined Swedish cohort of HIV-1 positive ECs with up to 20 years of clinical follow-up data.
Whole peripheral blood was obtained from three categories of individuals; a very well defined cohort of untreated HIV-1-positive EC (n=19), treatment naïve patients with viremia (VP, n=8) and HIV-1-negative persons (HC, n=14). Total RNAseq was performed using Illumina HiSeq2500 at the National Genomics Infrastructure, Science for Life Laboratory, Stockholm, Sweden. Variant calling was performed using the uniquely mapped duplicate-removed data to obtain unbiased variant frequency calls using Genome Analysis Tool Kit (GATK version 3.7). The duplicates were defined as the paired end reads where both mates map to the same genomic positions. Quality Score Recalibration (BQSR) using BaseRecalibrator module, which resulted in more accurate base qualities, to improve the accuracy of the variant calls. The report on callable loci was considered for the variant discovery. Finally, variant discovery was performed by UnifiedGenotyper module. The module used Bayesian genotype likelihood model to call the variants. HLA-typing was performed using seq2HLA_ver2.2.
We characterized EC with respect to class I HLA typing and variant calling in the AIDS restriction genes (ARGs). Among them, 63% (12/19) had at least one protective allele (A*25:01, A*74:01, B*14:02, B*27:05, B*42:01, B*51:01, B*57:01, B*57:03, B*58:01 and B*81:01) of whom four had two alleles. However, some of the EC also had disease-susceptible HLA alleles (B*07:01, B*08:0, B*35:03, B*53:01 etc). The single nucleotide polymorphisms (SNPs) in the HLA C region rs9264608, which has earlier been shown to have an independent protective effect, was observed in 21% (4/19) of EC and in 12% (1/8) of VP, but not in HC. While analyzing ARGs, no CCR5-Δ32 (rs333), CCR5 59029G (rs1799987), and SDF1-3’A (rs1801157) polymorphisms were not identified in any of the samples. However, HCP5 rs2395029, a SNP in the non-protein coding region, was observed in three of the EC. A Caucasian individual who was positive for the HCP5 rs2395029 was also positive for HLA B*57:01.
Our data suggest that protective HLA Class I alleles play a major role in EC status rather then the ARGs which has been reported earlier.