Objective:To establishment an assay for HIV-1 intact proviral DNA assay through droplet digital PCR (ddPCR).Methods:DNA was extracted by culturing 8E5 cells, a Tlymphocyte cell line containing a single copy of integrated HIV-1 provirus. Serial diluting DNA were prepared by amplified 1-fold, 5-fold, 25-fold, 625-fold, 3 125-fold, and 15 625-fold across the HIV-1 Ψ region, env region, and eukaryotic chromosome 10 RPP30 regions, and the linear relationship was calculated and the minimum detection concentration. DNA solution of 5 μl, 3.1 μl, 2.5 μl was added to the ddPCR mixture respectively, with each dilution undergoing two batches of detection, and each was repeated four times. The intra-batch variation coefficient was detected, while the inter-batch variation coefficient was detected by the same DNA amount and different DNA amounts to determine the stability; 8E5 cell was used to detect the intact proviral content in cells.Results:The linear fitting goodness of Ψ region, env region and RPP30 region are R2≥0.999, R2≥0.993, R2≥0.996 in 6 dilutions of DNA, respectively. At a 3 125-fold dilution, the lowest positive droplets were detected in the Ψ region, env region and RPP30 region were 3, 2 and 2, respectively, the detected concentrations were 2.37 copies/μl, 1.21 copies/μl and 1.58 copies/μl. The ddPCR repeatability experimental detecting DNA showed that the Ψ region of the intra-batch variation coefficients ranged from 0.66% to 3.43%, with the inter-batch variation coefficients of the same DNA at 3.19%, 4.3% and 3.45% respectively, and the inter-batch variation coefficients of the different DNA at only 4.35%. The env region of the intra-batch variation coefficients ranged from 0.7% to 3.20%, with the inter-batch variation coefficients of the same DNA at 3.18%, 4.52% and 3.4% respectively, and the inter-batch variation coefficients of the different DNA at only 4.02%. The RPP30 region of the intra-batch variation coefficients ranged from 0.91% to 2.91%, with the inter-batch variation coefficients of the same DNA at 3%, 4.55% and 3.37% respectively, and the inter-batch variation coefficients of the different DNA at only 3.98%. The proportion of 8E5 cells containing defective provirus and the proportion of intact provirus were calculated to be approximately 90% and 45%, respectively. Conclusions:Droplet digital PCR used to detect HIV-1 intact proviral DNA, showed strong stability and provided a technical means for HIV-1 infection reservoir detection.

Objective:To establish a method using activation-induced markers (AIM) to detect the function of HIV-1-specific CD4 + T cell subsets for evaluating the immune response of HIV-1-specific CD4 + T cells more effectively. Methods:Twelve chronically HIV-1-infected patients without antiviral therapy and six healthy people without HIV-1 infection were enrolled in this study. The function of HIV-1-specific T lymphocytes was detected by AIM and ICS based on polychromatic flow cytometry. The performance of the two methods in assessing HIV-1-specific CD4 + T cell immune response in HIV-1-infected patients was evaluated. Results:The positive rates of HIV-1-specific PD-1 + CD25 + CD4 + T, CD69 + CD200 + CD4 + T, CD69 + ICOS + CD4 + T, CD69 + ICOS + CD8 + T、CD137 + CD69 + CD8 + T、PD-1 + CD25 + CD8 + T and OX40 + PD-1 + CD8 + T cells in all of the HIV-1 patients were 11/12, 8/12, 7/12, 8/12, 8/12, 7/12 and 7/12 using AIM method. ICS results showed that the positive rates of HIV-1-specific IL-2 + CD4 + T, IFN-γ + CD4 + T, TNF-α + CD4 + T, IFN-γ + CD8 + T, TNF-α + CD8 + T and IL-2 + CD8 + T cells were 2/12, 2/12, 0, 12/12, 10/12 and 5/12, respectively. Conclusions:AIM method was more sensitive in antigen-specific CD4 + T cell detection, and could be used as a complementary method to ICS in assessing antigen-specific T cell response.

Objective:To analyze the characteristics of viral isolation and unique recombinant from untreated HIV-1 patients infected through sexual transmission and injection drug use, so as to provide evidence for understanding the biological characteristics and precise prevention and control of HIV-1 infection in different transmission routes.Methods:In view of the different HIV-1 transmission risks, newly diagnosed untreated HIV-1 patients from Beijing, Guangxi and Sichuan were carefully selected. Venous blood was collected to detect the viral load and CD4 + T cell count, and peripheral blood lymphocytes were isolated for virus isolation. Viral RNAs were extracted from the virus supernatant, and the near full-length genome sequences were obtained using in-house method, then the recombination patterns were determined. Results:Among the 65 HIV-1 infection, 32(49.2%), 20(30.8%) and 13(20.0%) were infected via men who have sex with men (MSM), heterosexual and injection drug use (IDU), respectively; genotypes mainly included 26(40.0%) CRF07_ BC, 23(35.4%) CRF01_ AE, and 9(13.8%) unique recombinant types (URFs). A total of 46 HIV-1 clinical strains were isolated. The positive rate of HIV-1 isolation was significantly negatively correlated with CD4 + T cells ( X2=4.22, P=0.04), but positively correlated with viral load ( X2=22.4, P<0.001); the multi-variate generalized estimating equations(GEE) model analysis of HIV-1 P24 antigen content showed similar result. In addition, GEE model showed a positive correlation between viral P24 antigen content and virus-producing culture time (52.14, 95% CI: 9.42~94.87, P=0.017). Viral growth curve analysis showed that the level of viral P24 antigen in MSM Group was significantly higher than that in heterosexual group and IDU group (adjusted P values were p<0.01 and P<0.05, respectively), on the 14th day after culture. The proportion of URFs in MSM Group was higher than that in heterosexual group, and the recombinant breakpoints in MSM Group were more than that in heterosexual group. Conclusions:MSM population was more sensitive to HIV-1 virus isolation; there was unique diversity of recombinant forms of HIV-1 among those with sexually transmitted infections, especially in the MSM population.

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 isolate HIV envelope specific monoclonal antibodies (mAbs) from a chronic HIV-1 subtype B′-infected individual with broadly neutralizing activity, and identify their binding activity, epitopes and neutralizing activity.Methods:Single B cell sorting were used to isolate antigen-specific B cells from an HIV-1 infected individual. Variable regions of heavy chain and light chain gene of mAbs were obtained by PCR amplification, and were ligated into the expression vector subsequently. After expression and purification of mAbs, the binding activity and neutralizing ability of mAbs were identified by ELISA and neutralization assay respectively.Results:Seven mAbs were obtained from the HIV-1 infected individual. The heavy chain genes of the mAbs are derived from IGHV1-69*09, IGHV1-08*01, IGHV1-46*01, IGHV4-34*01, IGHV4-61*01 and IGHV3-43*02 germline, SHM rates range from 10.76% to 21.05%. The light chain genes of the mAbs originate from IGKV3-20*01, IGKV1-39*01, IGKV1-NL1*01, IGKV3-15*01 and IGKV1-9*01 germline, SHM rates cover between 6.03% and 18.64%. Gp140 was well recognized by all seven antibodies. 508-B1, 508-C1, 508-C5, 508-D4 and 508-E5 are gp41-directed mAbs. 508-D6 and 508-F1 bind with gp120. 508-D4 and 508-F1 could neutralize pseudoviruses CNE8 and X2278 in Global Panel with IC 50 values of 38.1μg/ml and 41.7 μg/ml, respectively. Conclusions:This study successfully identified seven envelope specific mAbs, among them five mAbs are directed to gp41 region and two mAbs are targeted to gp120. Two mAbs showed limited neutralization spectrum. These mAbs may provide technical reserves for developing HIV-1 diagnostics kit, antibody-related drugs and vaccines.

HIV/AIDS has become a worldwide pandemic. It is crucial to develop new modes of treatment and prevention, since antiretroviral drugs cannot eradicate HIV infection. Broadly neutralizing antibodies (bnAb) are increasingly implicated in anti-HIV-1, and also shed light on the design of novel HIV-1 vaccines. In the following, we briefly review the progress in isolation and epitope specificity of broadly neutralizing antibodies against HIV-1.

Objective:To establish an in vitro growth competition assay using HIV-1 CRF07_BC infectious clone containing the mouse Thy1.1 gene or Thy1.2 gene. Methods:The mouse Thy1.1 gene and Thy1.2 gene were used to replace the 218 bases of Nef region of the CRF07_BC infectious clone (pXJDC6291-13) and construct the CRF07_BC infectious clones BCEA1 and BCEA2 plasmid. BCEA1 and BCEA2 plasmids were transfected into 293T to obtain the virus and the viral titration was measured. PM1 cells were co-infected with an equal virus. On the 3 rd to 6 th day of infection the cells were collected and labeled with specific antibodies Thy1.1 and Thy1.2. The viral fitness was detected by flow cytometry. Through "TFitness" (http: //bis.urmc.rochester.edu/vFitness) the relative viral fitness was calculated. The influence K103 N and K166R on the relative fitness of HIV-1 CRF07_BC were observed. Results:The relative fitness (1+ s) of CRF07_BC subtypes BCEA1 and BCEA2 viruses were 1.06±0.23693, which was not statistically significant. An in vitro growth competition assay for CRF07_BC was established. The in vitro growth competition assay was used to verify the relative fitness of the K103 N and K166R mutant strains to the wild strain. The relative fitness of BCEA2-K103 N/BCEA1 was 0.728282±0.16608, BCEA2-K166R/BCEA1 was 0.883385±0.19023, BCEA2-K103 N+ K166R/BCEA1 was 0.804604±0.06164. The relative fitness of K103 N resistant mutant strain and the wild strain was significantly different.Conclusions:An in vitro growth competition assay for the fitness of HIV-1 CRF07_BC virus was established. Based on the in vitro growth competition assay, the HIV-1 K103 N resistant mutant strain has reduced viral fitness.

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 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.

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.