Objective:To study the amino acid and codon usage profile of HIV-1 Env gene in donors whose serum exhibit highly broad cross-neutralizing activity. Methods:The samples were divided into highly broad cross-neutralizing activity group (hBCN + group) and non-highly broad cross-neutralizing activity group (hBCN - group) based on whether the neutralization breadth was higher than 90% or not. Full-length Env genes were amplified by single genome amplification (SGA) method from patients′ plasma samples, and the characteristics of Env sequences in hBCN + group were compared with hBCN - group. The correspondence analysis (COA) on relative amino acid usage (RAAU), adaptability to host based on similarity index D( A, B) and relative synonymous codon usage (RSCU) values of Env genes (hBCN + and hBCN -) with respect to human host RSCU were analyzed. Results:Correspondence analysis showed that the RAAU data of hBCN + group and hBCN - group were distributed along the two main axes to form two relatively separated clusters, indicating that the Env genes of the two groups had relatively unique amino acid usage patterns; the similarity index calculation results showed that hBCN + group (0.097) was lower than the hBCN - group (0.102), in addition, the Env gene of the hBCN + group had less frequency of similarly selected codons with human host system compared to hBCN - group. Conclusions:Env genes in hBCN + group and hBCN - group may have relatively unique amino acid usage patterns, and virus strains in hBCN + group are less adaptable to the host than those in hBCN - group.

Objective To predict the CTL epitopes of Tat exon 1 region in HIV-1 CRF07_BC strains, which were prevailing in China. Methods Total of 236 plasma samples were from the 3rd National HIV Molecular Epidemic Survey (NMES3). All the subjects were infected with HIV-1 CRF07_BC viruses. The tat exon 1 region was amplified by reverse transcription reaction and nested polymerase chain reaction (nested-PCR), then the PCR products were sequenced. The distribution of CTL epitopes of this region were predicted by on-line software BIMAS HLA Peptide Binding Predictions and statistics software. Results To-tal of 236 CRF07_BC strains were from 16 provinces, mainly in intravenous drug asers(58.9%)and then sex(25.0%). It was showed that there were 12 CTL epitopes of 236 Tat exon 1 region of CRF07_BC strains mainly located in proline-rich region, cysteine-rich region and core-region. Those epitopes were banded by 5 HLA presenting molecules in genotype(A * 2501 ,A * 2902, B * 15,B * 5301 and Cw * 1203) and 6 HLA presenting molecules in serotype (B53, B58 ,B57 ,A3 ,A68 and Cw12). The frequency of single amino acid substitution was more than 50% in 7 CTL epitopes. Conclusion The CTL epitopes in Tat exon 1 of CRF07 _BC strains were located in different functional regions, and there were some amino acid variations in them.

Objective To investigate the impact of HLA-A antigens carrying Bw4 epitopes on disease course of HIV-1 infection.Methods Three hundred and forty subjects chronically infected with HIV-I were recruited and their HLA-A and B alleles were genotyped with sequence-based high resolution typing assay.HLA-Bw genotypes of these HIV-1 infected subjects were determined and their association with CD+4 T cell counts and viral load were analysed.Results When compared with subjects canting no Bw4 epitopes in HLA-A and HLA-B loci (OBw4) (median of CD+4 T cell counts:294/μ1;plasma viral load median 6.29×104 copies/ml),CD+4 T cell counts in subjects with genotypes of 1Bw4-A and 2Bw4-AA were comparable (307 and 308/μ1,respectively),but higher viral load (1.53×105 and 2.68×105 copies/ml,respectively) was observed.In subjects with Bw4 epitopes in HLA-B alleles but no in HLA-A,significantly higher CD+4 T cell counts (417/μ1,P=0.013) and lower viral load (2.10×104 copies/ml,P=0.007) were observed compared with those without Bw4 in HLA-A and HLA-B.Conclusion HLA-B antigens carrying Bw4 epitope were protective in HIV-1 infection by maintaining higher CD+4 T cell counts and lower viral load,but such protective effect was not observed in HLA-A antigens earring Bw4 epitope.

Objective To explore the impact of broad antigen HLA-Bw4 on disease progression in HIV-1 infected subjects. Methods Three hundred and forty subjects chronically infected with HIV-1 and 69 HIV-1 negative subjects were recruited and HLA-B alleles were typed with sequence-based high resolution typing assay. HLA-Bw genotypes of these HIV-1 infected subjects were determined and their association with CD4+ T cell counts and viral loads were analyzed. Results Sixty-five HLA-B alleles were detected in HIV-1 positive subjects. Subjects with Bw4 (Bw4 homozygotes and Bw4Bw6 heterozygotes ) had higher CD4+ T cell counts ( P = 0. 004 ) and lower plasma viral load ( P = 0.003 ) than subjects without Bw4 ( Bw6 homozygotes). When compared with HIV-1 postive subjects with CD4+ T cell counts above 500 celis/μl, those with CD4+ T cell counts below 500 cells/μl were observed with decreased percentage of Bw4Bw6 heterozygote ( P =0.0002) and increased percentage of Bw6 homozygotes ( P < 0. 0001 ). There is no significant difference in CD4+ T cell counts between Bw4 homozygotes and Bw4Bw6 heterozygote, but lower viral loads were observed in Bw4Bw6 heterozygotes( P = 0. 037 ). Conclusion HLA-Bw4 can confer pretective effects on H1V-1 infected subjects by maintaining higher CD4+ T cell counts and lower viral load, the mechanism behind this effect need further exploration.

Objective To assess the impact of the virus on the complementary determining region 3 (CDR3) length diversity of T cell receptor(TCR) Vβ repertoires of CD4+ T lymphocytes and to explore its association with viral load in individuals with HIV-1 infection. Methods The TCR repertoire was examined using spectratyping of CDR3 length diversity within CD4+ T cells in HIV infected and healthy adults. Separation of CD4+ T cells from peripheral blood mononuclear cells ( PBMCs) was carried out by using immunomagnetic beads coated with anti-CD4 antibody. Total RNAs from the purified CD4 + T lymphocytes were isolated and used to perform nested-PCR amplifications in CDR3 of 22 TCR gene families. CDR3 diversity and its association with viral load in individuals with HIV-1 infection were analyzed. Results An average diversity for all CDR3 profiles in CD4+ T cells from 25 HIV-infected individuals was significantly different as compared to 10 age-matched healthy donors (P＜0.05) with the HIV-infected individuals losing diversity in the CDR3 profiles. There was positive correlation between changes in TCR CDR3 diversity and viral load (r = 0. 494, P ＜ 0. 05). The changes in CDR3 length diversity of Vβ families in HIV-infected individuals, particular in Vβ8, Vβ22, Vβ23 were statistically different from the healthy controls. Conclusion HIV-1 infection might induce the loss of TCR Vp repertoire diversity and disrupt the CDR3 Gaussian distributions within CD4 + T cells. There should be positive correlation between changes in TCR CDR3 diversity and the viral load in HIV-1 infected patients.

Objective To analyze characteristics of Nef-specific T lymphocyte responses in Chinese HIV-1 recombinant subtype B/C infectors. Methods 19 HIV-1 recombinant subtype B/C infectors infected within 1 year, 40 chronic infectors infected for more than 3 years were enrolled in this cohort study. Elispot assay was used to observe HIV-1 specific T lymphocyte responses in HIV-1 recombinant subtype B/C infectors. Results Nef-specific T lymphocyte responses of interferon-gamma secretion were identified in 15 Chinese HIV-1 recombinant subtype B/C infectors infected within 1 year. The specific T lymphocytes were mainly targeted at four peptides which span from Nef 83 to 135: EVA7081.1, EVAT081.5, EVA7081.6 and EVAT081.48. Responses were identified in 29(75. 2%) infectors with more than 3 years of infection and the specific T lymphocytes were mainly targeted at three peptides which span from Nef 63 to 101 : EVA7081.43, EVA7081.44, EVAT081.45, EVA7081.47, EVA7081.48 and EVA7081.49. The average magnitude of response in infectors with less than 1 year of infection was 284. 13 SFC/106 PBMC. The average magnitude of response in infectors with more than 3 years of infection was 152. 44 SFC/106 PBMC. There was a significant difference between the two groups (U = 91. 000, P = 0. 002). Conclusions HIV-1recombinant subtype B/C infectors at different stages of diseases (less than 1 year and more thank 3 years) can recognize central region of Nef. The magnitude of Nef-specific IFN-γ secretion T lymphocyte responses in this cohort gradually decrease with disease progression.

Objective To analyze the character of Pol-specific T lymphocyte responses and identify immunodominant region recognized in Chinese HIV-1 recombinant subtype B/C infectors at different stages of diseases. Methods Eleven Chinese HIV-1 recombinant subtype B/C infectors infected in 18 months, 25 which infected time more than 3 years and 10 HIV-1-seronegative healthy individuals were enrolled. HIV-1-specific T lymphocyte responses were analyzed by an IFN-γ ELISPOT assay against 249 overlapping peptides spanning HIV-1 Pol protein in the present study. Results Pol-specific T lymphocyte responses of IFN-γsecretion were identified in 8 (72.73%) out of 11 infectors infected in 18 months, the specific T lymphocytes are mainly targe-ted at six peptides which amino acid position from Pol 481 to 631 in reverse transcriptase region: Pol5581, Pol5582, Pol5587, Pol5609, Pol5610 and Pol5615. There was a negative correlation between the breadth of re-sponse and peripheral CD4+ T cell count (P=0.0212, r=-0.762) ; Responses were identified in 15 (60%) out of 25 chronic infectors, the specific T lymphocytes are mainly targeted at four peptides which amino acid po-sition from Pol 241 to 295: Pol5521, Pol5525, Pol5526, Pol5531 and another peptide: Pol5638 which amino acid position from Pol 708 to 722 in reverse transcriptase region. There was a positive correlation between the magnitude of Pol-specific IFN-γ secretion T lymphocyte responses and plasma viremia (P = 0.006 95 , r = 0.660) . None of the seronegative healthy individuals gave the positive responses. Conclusion Chinese HIV-1 recombinant subtype B/C infectors at different stages of diseases mainly recognized different re-gions of Pol.

Objective To analyze character of Nef-specific T lymphocyte responses in Chinese HIV-1 recombinant subtype C/B' and subtype B' infectors and to identify the common immunodominant re-gions recognized by these infectors. Methods Fifty-nine HIV-1 recombinant subtype C/B' infectors and 27 subtype B' infectors were tested by IFN-γ enzyme linked immunospot (ELISPOT) assay using HIV-1 C/B' Nef overlapping peptides. Results Nef-specific T-cell responses of IFN-γ secretion were identified in 44 (74.58%) out of 59 HIV-1 recombinant subtype C/B' infectors. Ten peptides, EVA7081.1,5, 6, 7,43, 44, 45, 47, 48, 49 were mainly recognized. Amino acid position was from Nef63 to 115 and 117 to 139. Twenty of 27 (74.07%) HIV-1 subtype B' infectors recognized peptides. EVA7081.1,2, 43 and 49 were mainly recognized. Amino acid position was from Nef 63 to 77 and 87 to 119. There was no correlation be-tween the Nef-specific IFN-production of HIV-1-specific T cells responses and viral load or CD4 T cell count in both subtype infectors. Conclusion The immunodominant regions, from Nef63 to 77 and 87 to 115 were recognized by both Chinese HIV-1 recombinant subtype C/B' infectors and subtype B' infectors. These re-gions could be used in design of vaccine.

Objective To explore the polymorphism of HLA class I alleles of HIV-infected former plasma donors and to investigate its impact on HIV-1 viral load in central China.Methods 106 subjects chronically infected with HIV-1 were recruited and HLA class I alleles were genotyped with PCR-SSP assay.HLA class I genotypes and haplotypes were determined and their association with plasma viral loads were analyzed.Gag-specific CTL responses were detected by an IFN-λ EUSPOT assay by using overlapping peptides,and their association with plasma viral loads were also analyzed.Results Subjects homozygous at HLA class I locus had higher plasma viral loads(P=0.0098);HLA-A*30,-B*13,-Cw*06,-Cw*14 alleles and HLA-A*30/B*13/Cw*06 haplotype were associated with lower plasma viral loads(P=0.0004,0.0103,0.0058,0.0371 and 0.0006);an inverse correlation between p2p7p1p6-specific CTL responses and viral loads in subjects with HLA-A*30/B*13/Cw*06 haplotype as well as an inverse correlation between p17-specific CTL responses and viral loads in subjects with HLA-Cw*14 allele were observed.Conclusion HLA-A*30,-B*13,-Cw*06,-Cw*14 alleles and HLA-A*30/B*13/Cw*06 haplotype were associated with lower plasma viral loads and Gag-specific CTL responses restricted by these HLA alleles may contribute to the protection.

The ELISPOT assay is increasingly used for assessing cellular immune responses in clinical trials of HIV-1 or cancer vaccines. However, to date, data from clinical trials do not consistently show that immune responses are correlated with clinical endpoints. This is due in part to the lack of assay standardization and validation across laboratories and therefore, a quality control panel is required to establish competency and comparability amongst different laboratories. In this study peripheral blood mononuclear cells (PBMCs) from healthy individuals were screened and frozen in liquid nitrogen. The recovery and viability of the PBMCs and the frequencies of interferon (IFN)-γ-secreting cells after CEF peptide pool stimulation were detected after various intervals in seven different laboratories. The recovery and viability did not differ significantly after different intervals. Although the frequencies of IFN (interferon)-γ-secreting cells among thawed PBMCs (peripheral blood mononuclear cells) fluctuated after CEF peptide pool stimulation at different intervals, they were not significantly decreased compared with those among fresh PBMCs. However, the viabilities, recoveries and frequencies of IFN-γ-secreting cells differed significantly among the seven laboratories. Our results indicate that cryopreserved PBMCs could be used as a quality control panel for ELISPOT. However, the procedures for ELISPOT need to be standardized amongst different laboratories.