Kunxue Hong State Key Laboratory for Infectious Disease Control and Prevention

1. Majority of Naturally Infected HIV-1 Induced CTL Responses Targeting HIV-1 Location With Recorded HLA-I Restricted Epitopes Kunxue Hong State Key Laboratory for Infectious Disease Control and Prevention National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention Beijing 100050, China

2. Background • To construct vaccine aiming to elicit effective CTL responses against HIV-1, the immunogenic regions which can be targeted by CTL responses mounting to naturally infected cells with virus should be referred to. • HIV Molecular Database have been compiled for the currently reported CD8+ CTL epitopes restricted by specified HLA-I alleles. • By using the dataset generated in a HARRT free Chinese population infected with HIV-1 clade B’ or CRF07_BC, the coverage of the HIV Molecular Database were evaluated Study Design • Study population: • 60 subjects primarily infected with HIV-1 CRF07_BC and 166 subjects chronically infected with HIV-1 clade B were enrolled • Dataset: • HLA class I typing data: for loci A,B and C, sequence based high resolution typing. • ELISPOT data: using 2 sets of OLPs covering whole proteome of HIV-1 clades B and C were used as test peptides (413 ×2=826 OLPs, 15~20 mer, overlapping by 10 amino acids), and CTL responses at single OLP level were measured in 2 round ELISPOT assays. • All of OLPs used in this study were analyzed with web-based ELF program (http://www.hiv.lanl.gov/content/sequence/ELF/epitope_analyzer.html) and recorded epitopes were annotated with epitope abbreviation and its corresponding HLA restriction.

3. Summary of dataset used in this study • 8037 CTL responses were detected above positive criteria (>50 SFC/106 PBMC after substracting background and at least 3 times the mean number of SFC of the three control wells). • 740 OLPs (89.59%) were targeted by the detected 8037 CTL responses (361 clade B OLPs <87.41%> and 379 clade C OLPs <91.77%> )

4. HLA-I Allele Frequency of the study population HLA-A HLA-B HLA-C

5. Classification of CTL responses based on characteristics of test OLPs

6. Analysis of CTL responses targeting OLPs containing reported HLA-I restricted epitopes 1 Based on the comparison of the amino acid sequence of test OLPs and reported epitopes. 2 All of the 6 HLA-I alleles of the subject mounting the CTL responses are not reported in the record of defined epitopes. 3 At least one of the 6 HLA-I alleles of the subject mounting the CTL responses matched with reported restriction of the defined epitopes

7. Summary 8037 CTL responses targeting 740 OLPs derived from HIV-1 clades B and C proteome were detected in 226 Chinese subjects 72.12% of the responses targeted OLPs with defined CTL epitopes in LANL HIV Immunology Database, and another 16.18% of the responses targeted OLPs containing variance form of defined CTL epitopes For the CTL responses targeting OLPs with defined CTL epitopes, the HLA-I restriction of at least 36.94% of them are other than the reported alleles in LANL HIV Immunology Database Majority of naturally infected HIV-1 induced CTL responses targeting HIV-1 location with recorded HLA-I restricted epitopes, which are recorded in the LANL HIV Immunology Database The promiscuity of HLA-I restriction in CTL epitopes are of great level, which may be underestimated in previous studies

8. Acknowledgement • Local CDC in Xinjiang, Sichuan,Henan and Anhui • NCAIDS Laboratory • Jianping Chen • Mingming Jia • Yiming Shao • Tangdu Hospital • Yongtao Sun • Nankai University • Yichen Lu • Partners AIDS Research Center • Xu Yu • Altfeld Marcus • Bruce D. Walker • This study was supported in part by the National Institutes of Health (NIH Contract No.Nol-AL-30024)