Genetic and neutralization properties of HIV-1 env clones from subtype B/BC/AE infections in China

Construction and Characterization of HIV-1 env-Pseudoviruses of the Recombinant Form CRF63_02A and Subtype A6

HIV-1 env-pseudoviruses are a useful tool in the search for antiviral drugs (entry inhibitors) and evaluation of the efficacy of HIV-1 vaccines. Given the high genetic variability of HIV-1, it is necessary to regularly update the panels of pseudoviruses in accordance with the emergence of new strains. Based on genetic variants of HIV-1 circulating in the regions of the Siberian Federal District, 13 HIV-1 env-pseudoviruses of recombinant form CRF63_02A and subtype A6 were obtained. Most pseudoviruses have been shown to be sensitive to neutralization by bnAbs VRC01, PGT126, and 10E8, moderately sensitive to bnAbs PG9 and 4E10, and resistant to bnAbs 2G12, PG16, and 2F5. All obtained variants of pseudoviruses are CCR5-tropic.

HIV-1 pseudoviruses constructed in China regulatory laboratory

To better evaluate HIV-1 vaccines and therapeutics, the National Institutes for Food and Drug Control of China developed a panel of HIV-1 pseudoviruses including 462 viral strains derived from China, covering the majority of contemporaneous subtypes and circulating recombinant forms. Compared with the standard pseudovirus panels derived from other countries/regions, the Chinese isolates are more susceptible to neutralization by the sera obtained in China, revealing the strain/subtype specificity. Some of these pseudoviruses have already been used for the evaluation of HIV vaccines and drug candidates in Chinese clinical trials. The pseudoviruses panel is widely shared with interested scientists involved in the research and development of vaccines and antiviral drugs against HIV-1 strains prevalent in China.

Evaluation of susceptibility of HIV-1 CRF01_AE variants to neutralization by a panel of broadly neutralizing antibodies

Broadly neutralizing antibodies (bNAbs) are very promising agents for HIV-1 prophylaxis and AIDS treatment. However, the neutralization susceptibility of circulating recombinants such as CRF01_AE, which is becoming increasingly prevalent, has not been studied in detail until now. Here, we focused on CRF01_AE in China and aimed to find bNAbs that can be used for neutralization of CRF01_AE. Full-length env clones were obtained from the plasma samples of 22 HIV-1-infected individuals sampled in 2009 and 2015. An env-pseudovirus-based neutralization assay was conducted using five categories of bNAbs: VRC01, NIH45-46^G54W, and 3BNC117 (targeting the CD4 binding site); PG9 and PG16 (targeting the V1V2 loop); 2G12 (glycan specific), PGT121 and 10-1074 (targeting the V3 glycan); 2F5, 4E10, and 10E8 (targeting the membrane-proximal external region (MPER)). The neutralizing efficiency was compared, and features of the escape pseudoviruses were analyzed. The CRF01_AE pseudoviruses exhibited different susceptibility to these bNAbs. Overall, 4E10, 10E8, and 3BNC117 neutralized all 22 env-pseudotyped viruses, followed by NIH45-46^G54W and VRC01, which neutralized more than 90% of the viruses. 2F5, PG9, and PG16 showed only moderate breadth, while the other three bNAbs neutralized none of these pseudoviruses. Specifically, 10E8, NIH45-46^G54Wand 3BNC117 showed the highest efficiency, combining neutralization potency and breadth. Mutations at position 160, 169, 171 were associated with resistance to PG9 and PG16, while loss of a potential glycan at position 332 conferred insensitivity to V3-glycan-targeting bNAbs. Our results may help for choosing bNAbs that can be used preferentially for prophylactic or therapeutic approaches in China.

Comparison of the genotypic and phenotypic properties of HIV-1 standard subtype B and subtype B/B' env molecular clones derived from infections in China

Although a number of standardized human immunodeficiency virus 1 (HIV-1) pseudoviruses have been generated to assess neutralizing antibodies, subtype B/B′ has not been comprehensively characterized either genotypically or phenotypically. Full-length env genes were isolated from plasma samples derived from B/B′-infected individuals, including former plasma donors and men who had sex with men. The neutralization properties of these pseudoviruses were determined by testing against sCD4, 16 neutralizing monoclonal antibodies and 44 plasma samples, including samples from those infected with the three major prevalent clades in China. Twenty-eight pseudoviruses were successfully constructed, including 15 B′ and 13 B strains. Compared with subtype B strains from North America and Europe, the B′ strains from China showed greater variation in the V3 loop and higher susceptibility to the neutralizing antibody 2F5 and B/B′ plasma samples. The B′ strains from China showed significantly lower susceptibility to some trimer apex-binding neutralizing antibodies (PGT145, CH01, CH02, CH03, and CH04) than the B strains from Western countries. The 28 B-pseudotyped and B′-pseudotyped viruses were grouped into high, medium, and low clusters based on their overall neutralization sensitivity to plasma samples. The different genotypic and phenotypic properties of the standard subtype B from those of the Western viruses compared to the B and B′ strains from China suggest that clones from HIV-1-infected individuals in China are more suitable for the evaluation of candidate vaccines targeting the subtype B/B′ viruses circulating in China.

Development and optimization of a sensitive pseudovirus-based assay for HIV-1 neutralizing antibodies detection using A3R5 cells

Sensitive assays for HIV-1 neutralizing antibody detection are urgently needed for vaccine immunogen optimization and identification of protective immune response levels. In this study, we developed an easy-to-use HIV-1 pseudovirus neutralization assay based on a human CD4⁺ lymphoblastoid cell line A3R5 by employing a high efficient pseudovirus production system. Optimal conditions for cell counts, infection time, virus dose and concentration of DEAE-dextran were tested and identified. For T-cell line-adapted tier 1 virus strains, significantly higher inhibitory efficiency was observed for both monoclonal neutralizing antibody (4 fold) and plasma (2 fold) samples in A3R5 than those in TZM-bl assay. For circulating tier 2 strains, the A3R5 pseudovirus assay showed even much higher sensitivity for both neutralizing antibody (10 fold) and plasma (9 fold) samples. When sequential neutralizing antibody seroconverting samples were tested in both A3R5 and TZM-bl assays, the seroconverting points could be detected earlier for tier 1 (15.7 weeks) and tier 2 (68.3 weeks) strains in A3R5 assay respectively. The high sensitive pseudovirus assay using more physiological target cells could serve as an alternative to the TZM-bl assay for evaluation of vaccine-induced neutralizing antibodies and identification of the correlates of protection.

Development and application of a bioluminescent imaging mouse model for Chikungunya virus based on pseudovirus system

Chikungunya virus (CHIKV) is an arthropod-borne virus that is transmitted to humans primarily via the bite of an infected mosquito. Infection of humans by CHIKV can cause chikungunya fever which is an acute febrile illness associated with severe, often debilitating polyarthralgias. Since a re-emergence of CHIKV in 2004, the virus has spread into novel locations in nearly 40 countries including non-endemic regions and has led to millions of cases of disease throughout countries. Handling of CHIKV is restricted to the high-containment Biosafety Level 3 (BSL-3) facilities, which greatly impede the research progress of this virus. In this study, an envelope-pseudotyped virus expressing the firefly luciferase reporter protein (pHIV-CHIKV-Fluc) was generated. An in vitro sensitive neutralizing assay and an in vivo bioluminescent-imaging-based mouse infection model had been developed based on the CHIKV pseudovirus. Utilizing the platform, protection effect of DNA vaccine was evaluated. Therefore, this study provides a safe, sensitive and visualizing model for evaluating vaccines and antiviral therapies against CHIKV in low containment BSL-2 laboratories.

Escape from humoral immunity is associated with treatment failure in HIV-1-infected patients receiving long-term antiretroviral therapy

Interindividual heterogeneity in the disease progression of HIV-1-infected patients receiving long-term antiretroviral therapy suggests that some host-related factors may have limited treatment efficacy. To understand the nature of factors contributing to treatment failure, we performed a retrospective cohort study of 45 chronically HIV-1-infected individuals sharing a similar demographics and route of infection, compared the differences between virologically suppressed (VS) and treatment failure (TF) patients with respect to clinical, immunological and virological characteristics. We found that the baseline diversity of HIV-1 env quasispecies was the major difference between VS and TF group, and higher baseline diversity in TF patients. We further predicted TF-related env mutations using a selection pressure-based approach, followed by an analysis of these mutations based on the available three-dimensional structures of gp120/gp41 or their complexes with neutralizing antibodies. Notably, almost all of the identified residues could be mapped to the epitopes of known HIV-1 neutralizing antibodies, especially the epitopes of broadly neutralizing antibodies, and these mutations tended to compromise antibody-antigen interactions. These results indicate that the escape of HIV-1 from host humoral immunity may play a direct role in TF in long-term antiretroviral-experienced patients and that based on env gene sequence of the viruses in the patients.

Development of in vitro and in vivo rabies virus neutralization assays based on a high-titer pseudovirus system

Pseudoviruses are useful virological tools because of their safety and versatility; however the low titer of these viruses substantially limits their wider applications. We developed a highly efficient pseudovirus production system capable of yielding 100 times more rabies pseudovirus than the traditional method. Employing the high-titer pseudoviruses, we have developed robust in vitro and in vivo neutralization assays for the evaluation of rabies vaccine, which traditionally relies on live-virus based assays. Compared with current rapid fluorescent focus inhibition test (RFFIT), our in vitro pseudovirus-based neutralization assay (PBNA) is much less labor-intensive while demonstrating better reproducibility. Moreover, the in vivo PBNA assay was also found to be superior to the live virus based assay. Following intravenous administration, the pseudovirus effectively infected the mice, with dynamic viral distributions being sequentially observed in spleen, liver and brain. Furthermore, data from in vivo PBNA showed great agreement with those generated from the live virus model but with the experimental time significantly reduced from 2 weeks to 3 days. Taken together, the effective pseudovirus production system facilitated the development of novel PBNA assays which could replace live virus-based traditional assays due to its safety, rapidity, reproducibility and high throughput capacity.

Effect of the maturation of neutralizing antibodies on human immunodeficiency virus (HIV) envelope evolution in HIV-infected subjects

Delineating the course of NAb (neutralizing antibody) development in natural infection may provide clues for NAb-targeted HIV-1 vaccine design. Two subjects, A (non-neutralizer) and E (neutralizer), were chosen from 75 HIV-1 positive subjects of a MSM (men who have sex with men) cohort to investigate the key events of virus evolution in the development course of neutralizing antibodies. Pseudovirus quasispecies (at least 10 strains) were generated for each time points of the infection course. The diversity and divergence of the env quasispecies per time point for subject E were significantly higher than those for subject A (p<0.05). Compared with subject A, the gp160 derived from subject E acquired longer V1V2 region and more N-glycans during the development of neutralizing antibodies. The developing course of neutralizing antibody lagged behind the virus evolution, of which the pseudoviruses could only been neutralized by the latter time-point sera. The neutralization-driven evolution of the virus for subject E was mostly mapped to the C1-C3 region of gp160. Through site-directed mutagenesis, some key sites and region were identified to be associated with the virus escape, including: Q85P, H183P, K340E, L365S, L369I, I372V and insertions of 355N in C3 and NITDEVKIG in V1 region.

N463 Glycosylation Site on V5 Loop of a Mutant gp120 Regulates the Sensitivity of HIV-1 to Neutralizing Monoclonal Antibodies VRC01/03

BACKGROUND

HIV-1 gp120/gp41 is heavily modified by n-linked carbohydrates that play important roles either in correct folding or in shielding vulnerable viral protein surfaces from antibody recognition.

METHODS

In our previous work, 25 potential N-linked glycosylation sites (PNGS) of a CRF07_BC isolate of HIV-1 were individually mutated, and the resulting effects on infectivity and antibody-mediated neutralization were evaluated. To further understand the functional role of these PNGS, we generated double and multiple mutants from selected individual PNGS mutants. The effects were then evaluated by examining infectivity and sensitivity to antibody-mediated neutralization by neutralizing monoclonal antibodies (nMAbs) and serum antibodies from HIV-1 positive donors.

RESULTS

Infectivity results showed that, among the 12 combined PNGS mutants, only 197M.1 (N197D/N301Q) lost infectivity completely, whereas all others (except for 197M.6) showed reduced viral infectivity. In terms of neutralization sensitivity to known nMAbs, we found that adding N463Q mutation to all the gp120 mutants containing N197D significantly increased neutralization sensitivity to VRC01 and VRC03, suggesting N197 and N463 have a strong synergistic effect in regulating the neutralizing sensitivity of HIV-1 to the anti-CD4bs nMAbs VRC01/VRC03. Structural analysis based on the available structures of gp120 alone and in complex with CD4 and various nMAbs elucidates a molecular rationale for this experimental observation.

CONCLUSIONS

The data indicate that N463 plays an important role in regulating the CD4bs MAbs VRC01/VRC03 sensitivity in the genetic background of N197D mutation of gp120, which should provide valuable information for a better understanding of the interplay between HIV-1 and VRC01/03.

Cross-neutralizing antibody profile of Chinese HIV-1-infected individuals and the viral envelope features from elite neutralizers

OBJECTIVE

Knowledge about the profile of neutralization responses and the viral envelope features of HIV-1-infected individuals in China may provide new insights for vaccine design against local viruses.

METHODS

Eight hundred sixty plasma samples from antiretroviral treatment-naive HIV-1-infected individuals in Xinjiang province (611) and Guangxi province (249), who had acquired infection over 3 years through intravenous drug use or sexual contact, were examined for their ability to neutralize diverse envelope-pseudoviruses of 5 subtypes. The sequence features of the envelopes from elite neutralizers were analyzed.

RESULTS

From Xinjiang and Guangxi, 29.1% and 5.2% of plasmas displayed intrasubtype cross neutralization against subtype B and subtype C, respectively. From Xinjiang, 10.6% of the plasmas displayed broad neutralization against the 3 subtypes, B, C, and CRF01_AE; whereas only 2.4% from Guangxi displayed broad neutralization. Envelopes from 6 elite neutralizers were obtained by single-genome amplification. The variations of their envelopes including the lengths, glycans, and net charges in V1, V2, and V4 regions were compared with those from CRF07_BC env sequences from the HIV Sequence Database. The Envs from 3 elite neutralizers displayed the sensitivities to the monoclonal broadly neutralizing antibodies such as PG9, PG16, and 4E10. Some unique characteristics of the envelope glycoproteins from the Chinese elite neutralizers were found.

CONCLUSIONS

The neutralization profile of HIV-1-infected individuals in the 2 regions of China, where the HIV-1 subtypes are the representative in China, and the unique characteristics of the envelope glycoproteins from the Chinese elite neutralizers provide useful information for viral infection prevention and an insight for vaccine design against locally epidemic viruses.

Three amino acid residues in the envelope of human immunodeficiency virus type 1 CRF07_BC regulate viral neutralization susceptibility to the human monoclonal neutralizing antibody IgG1b12

The CD4 binding site (CD4bs) of envelope glycoprotein (Env) is an important conserved target for anti-human immunodeficiency virus type 1 (HIV-1) neutralizing antibodies. Neutralizing monoclonal antibodies IgG1 b12 (b12) could recognize conformational epitopes that overlap the CD4bs of Env. Different virus strains, even derived from the same individual, showed distinct neutralization susceptibility to b12. We examined the key amino acid residues affecting b12 neutralization susceptibility using single genome amplification and pseudovirus neutralization assay. Eleven amino acid residues were identified that affect the sensitivity of Env to b12. Through site-directed mutagenesis, an amino acid substitution at position 182 in the V2 region of Env was confirmed to play a key role in regulating the b12 neutralization susceptibility. The introduction of V182L to a resistant strain enhanced its sensitivity to b12 more than twofold. Correspondingly, the introduction of L182V to a sensitive strain reduced its sensitivity to b12 more than tenfold. Amino acid substitution at positions 267 and 346 could both enhance the sensitivity to b12 more than twofold. However, no additive effect was observed when the three site mutageneses were introduced into the same strain, and the sensitivity was equivalent to the single V182L mutation. CRF07_BC is a major circulating recombinant form of HIV-1 prevalent in China. Our data may provide important information for understanding the molecular mechanism regulating the neutralization susceptibility of CRF07_BC viruses to b12 and may be helpful for a vaccine design targeting the CD4bs epitopes.

A systematic study of the N-glycosylation sites of HIV-1 envelope protein on infectivity and antibody-mediated neutralization

Background

Glycans on the human immunodeficiency virus (HIV) envelope glycoprotein (Env) play an important role in viral infection and evasion of neutralization by antibodies. In this study, all 25 potential N-linked glycosylation sites (PNGS) on the HIV-1 CRF07_BC Env, FE, were mutated individually to study the effect of their removal on viral infectivity, virion production, and antibody-mediated neutralization.

Results

Removal of specific N-glycosylation sites has a significant effect on viral infectivity and antibody-mediated neutralization phenotype. Six of these glycosylation mutants located on the V1/V2 and C1/C2 domains lost infectivity. PNGS mutations located on V4/C4/V5 (except N392 on V4), were shown to increase viral infectivity. Furthermore, FE is much more dependent on specific glycans than clade B Env YU-2. On neutralization effect, PNGS mutations at N197 (C2), N301 (V3), N442 (C4) and N625 (gp41) rendered the virus more susceptible to neutralization by the monoclonal antibodies (MAbs) that recognize the CD4 binding site or gp41. Generally, mutations on V4/V5 loops, C2/C3/C4 regions and gp41 reduced the neutralization sensitivity to PG16. However, mutation of N289 (C2) made the virus more sensitive to both PG9 and PG16. Furthermore, we showed that mutations at N142 (V1), N355 (C3) and N463 (V5) conferred resistance to neutralization by anti-gp41 MAbs. We used the available structural information of HIV Env and homology modeling to provide a structural basis for the observed biological effects of these mutations.

Conclusions

This report provides the first systematic experimental account of the biological role of the entire PNGS on an HIV-1 Env, which should provide valuable insights for understanding the function of Env in HIV infection cycle and for developing future anti-HIV strategies.

Severe fever with thrombocytopenia virus glycoproteins are targeted by neutralizing antibodies and can use DC-SIGN as a receptor for pH-dependent entry into human and animal cell lines

Severe fever with thrombocytopenia syndrome virus (SFTSV) is a novel bunyavirus that recently emerged in China. Infection with SFTSV is associated with case-fatality rates of up to 30%, and neither antivirals nor vaccines are available at present. Development of antiviral strategies requires the elucidation of virus-host cell interactions. Here, we analyzed host cell entry of SFTSV. Employing lentiviral and rhabdoviral vectors, we found that the Gn/Gc glycoproteins (Gn/Gc) of SFTSV mediate entry into a broad range of human and animal cell lines, as well as human macrophages and dendritic cells. The Gn/Gc proteins of La Crosse virus (LACV) and Rift Valley Fever Virus (RVFV), other members of the bunyavirus family, facilitated entry into an overlapping but not identical range of cell lines, suggesting that SFTSV, LACV, and RVFV might differ in their receptor requirements. Entry driven by SFTSV Gn/Gc was dependent on low pH but did not require the activity of the pH-dependent endosomal/lysosomal cysteine proteases cathepsins B and L. Instead, the activity of a cellular serine protease was required for infection driven by SFTSV and LACV Gn/Gc. Sera from convalescent SFTS patients inhibited SFTSV Gn/Gc-driven host cell entry in a dose-dependent fashion, demonstrating that the vector system employed is suitable to detect neutralizing antibodies. Finally, the C-type lectin DC-SIGN was found to serve as a receptor for SFTSV Gn/Gc-driven entry into cell lines and dendritic cells. Our results provide initial insights into cell tropism, receptor usage, and proteolytic activation of SFTSV and will aid in the understanding of viral spread and pathogenesis.

Comparison on virulence and immunogenicity of two recombinant vaccinia vaccines, Tian Tan and Guang9 strains, expressing the HIV-1 envelope gene

BACKGROUND

The vaccinia virus Guang9 strain (VG9), derived from the vaccinia virus Tian Tan strain (VTT) has been found to be less virulent than VTT.

METHODOLOGY/PRINCIPAL FINDINGS

To investigate whether VG9 could be a potential replicating virus vector, the TK genes in VG9 and VTT were replaced with the HIV-1 envelope gene via homologous recombination, resulting in the recombinant viruses, VG9-E and VTT-E. The biology, virulence, humoral and cellular immunological responses of VG9-E and VTT-E were evaluated. Our results indicated no obvious difference in range of host cells and diffusion between two recombinant viruses. Neurovirulence for VG9-E in weanling and suckling mice, and skin virulence in rabbits, were lower than that of VTT-E. The humoral immune responses, including binding antibody and neutralizing antibody responses, induced by VG9-E were not significantly different from those for VTT-E whilst IFN-γ response which represented cellular immune response induced by VG9-E was significantly higher than that did by VTT-E.

CONCLUSIONS/SIGNIFICANCE

Our results indicated that VG9-E was less virulent, yet induced higher cellular immune response than VTT-E. Therefore, it could be an ideal replicating vaccinia vector for HIV vaccine research and development.

DNA prime-protein boost using subtype consensus Env was effective in eliciting neutralizing antibody responses against subtype BC HIV-1 viruses circulating in China

Previously, we have shown that DNA prime-protein boost is effective in eliciting neutralizing antibodies (NAb) against randomly selected HIV-1 isolates. Given the genetic diversity of HIV-1 viruses and the unique predominant subtypes in different geographic regions, it is critical to test the DNA prime-protein boost approach against circulating viral isolates in key HIV endemic areas. In the current study, the same DNA prime-protein boost vaccine was used as in previous studies to investigate the induction of NAb responses against HIV-1 clade BC, a major subtype circulating in China. A codon optimized gp120-BC DNA vaccine, based on the consensus envelope (Env) antigen sequence of clade BC, was constructed and a stable CHO cell line expressing the same consensus BC gp120 protein was produced. The immunogenicity of this consensus gp120-BC was examined in New Zealand White rabbits by either DNA prime-protein boost or protein alone vaccination approaches. High levels of Env-specific antibody responses were elicited by both approaches. However, DNA prime-protein boost but not the protein alone immune sera contained significant levels of NAb against pseudotyped viruses expressing HIV-1 BC Env antigens. Furthermore, high frequencies of CD4 binding site-targeted antibodies were found in the DNA prime- protein boost rabbit sera indicating that the positive NAb may be the result of antibodies against conformationally sensitive epitopes on HIV-1 Env. The findings support that DNA prime-protein boost was effective in eliciting NAb against a key HIV-1 virus subtype in China. This result may lead to the development of regional HIV vaccines through this approach.

Phenotypic analysis of HIV-1 genotypic drug-resistant isolates from China, using a single-cycle system

BACKGROUND AND OBJECTIVES

Drug resistance in HIV-1 is one of the main causes of failure of antiretroviral therapy. Phenotypic detection of drug-resistant HIV-1 can provide guidance in selecting the optimal treatment regimen. Traditional phenotype assays are labor intensive and time consuming. Thus, a rapid and convenient phenotype assay with a single cycle of replication was developed and used in this study.

METHODS

Two restriction endonuclease sites, ApaI and AgeI, were inserted into the plasmid pSG3Δenv(,) using site-directed mutagenesis. The reverse transcriptase and protease genes of HIV-1 were amplified from patients and cloned into the modified pSG3Δenv. Sixteen original recombinant pseudoviruses were generated. The phenotypic susceptibility of these 16 recombinant pseudoviruses to 12 antiretroviral drugs was determined using a luciferase reporter system, and the phenotype and genotype results were compared.

RESULTS

A modified phenotype assay with a single-cycle system was established, and its reproducibility and feasibility were validated. Approximately 89% of the phenotype results were in agreement with the genotype results; this slight disagreement may have been due to complex and multiple resistance mutations. The phenotype results showed that individual pseudoviruses with four thymidine analog mutations (TAMs).[M41L, T67N, L210W, and T215Y] in combination with various other mutations had different levels of resistance to nucleoside reverse transcriptase inhibitors (NRTIs). Mutations E44A, T69D, and V118I influenced the pattern of resistance of TAMs. The level of resistance to non-NRTIs (NNRTIs) was also variable when different NNRTI-resistance mutations were combined.

CONCLUSION

The single-cycle pseudovirus phenotypic susceptibility detection system reflects HIV-1 drug resistance, especially for complex resistance mutants, and could be used to screen new antiretroviral candidates.

HIV-1 neutralization coverage is improved by combining monoclonal antibodies that target independent epitopes

HIV-1 neutralizing monoclonal antibodies (MAbs) define key targets for vaccine development and are being considered for passive prevention of infection. We analyzed the interaction of MAbs to two independent epitopes on the viral envelope glycoprotein. Potently neutralizing MAbs to the CD4 binding site and V1V2 region displayed no in vitro cross-competition and displayed additive, though not synergistic, neutralization activity. Predicted neutralization coverage of a combination of two MAbs reached 97% on a 208-isolate panel.

Broad antiviral activity and crystal structure of HIV-1 fusion inhibitor sifuvirtide

Sifuvirtide (SFT) is an electrostatically constrained α-helical peptide fusion inhibitor showing potent anti-HIV activity, good safety, and pharmacokinetic profiles, and it is currently under phase II clinical trials in China. In this study, we demonstrate its potent and broad anti-HIV activity by using diverse HIV-1 subtypes and variants, including subtypes A, B, and C that dominate the AIDS epidemic worldwide, and subtypes B', CRF07_BC, and CRF01_AE recombinants that are currently circulating in China, and those possessing cross-resistance to the first and second generation fusion inhibitors. To elucidate its mechanism of action, we determined the crystal structure of SFT in complex with its target N-terminal heptad repeat region (NHR) peptide (N36), which fully supports our rational inhibitor design and reveals its key motifs and residues responsible for the stability and anti-HIV activity. As anticipated, SFT adopts fully helical conformation stabilized by the multiple engineered salt bridges. The designing of SFT also provide novel inter-helical salt bridges and hydrogen bonds that improve the affinity of SFT to NHR trimer. The extra serine residue and acetyl group stabilize α-helicity of the N-terminal portion of SFT, whereas Thr-119 serves to stabilize the hydrophobic NHR pocket. In addition, our structure demonstrates that the residues critical for drug resistance, located at positions 37, 38, 41, and 43 of NHR, are irreplaceable for maintaining the stable fusogenic six-helix bundle structure. Our data present important information for developing SFT for clinical use and for designing novel HIV fusion inhibitors.

Susceptibility of HIV-1 subtypes B', CRF07_BC and CRF01_AE that are predominantly circulating in China to HIV-1 entry inhibitors

Background

The B′, CRF07_BC and CRF01_AE are the predominant HIV-1 subtypes in China. It is essential to determine their baseline susceptibility to HIV entry inhibitors before these drugs are used in China.

Methodology/Principal Findings

The baseline susceptibility of 14 representative HIV-1 isolates (5 CRF07_BC, 4 CRF01_AE, and 5 B′), most of which were R5 viruses, obtained from drug-naïve patients to HIV entry inhibitors, including two fusion inhibitors (enfuvirtide and C34), two CCR5 antagonists (maraviroc and TAK779) and one CXCR4 antagonist (AMD3100), were determined by virus inhibition assay. The sequences of their env genes were amplified and analyzed. These isolates possessed similar susceptibility to C34, but they exhibited different sensitivity to enfuvirtide, maraviroc or TAK779. CRF07_BC isolates, which carried polymorphisms of A578T and V583I in the N-terminal heptad repeat and E630Q, E662A, K665S, A667K and S668N in the C-terminal heptad repeat of gp41, were about 5-fold less sensitive than B′ and CRF01_AE isolates to enfuvirtide. Subtype B′ isolates with a unique polymorphism site of F317W in V3 loop, were about 4- to 5-fold more sensitive than CRF07_BC and CRF01_AE isolates to maraviroc and TAK779. AMD3100 at the concentration as high as 5 µM exhibited no significant inhibitory activity against any of the isolates tested.

Conclusion

Our results suggest that there are significant differences in baseline susceptibility to HIV entry inhibitors among the predominant HIV-1 subtypes in China and the differences may partly result from the naturally occurring polymorphisms in these subtypes. This study provides useful information for rational design of optimal therapeutic regimens for HIV-1-infected patients in China.

Genetic and neutralization sensitivity of diverse HIV-1 env clones from chronically infected patients in China

As HIV-1 continues to spread in China from traditional high risk populations to the general public, its genetic makeup has become increasingly complex. However, the impact of these genetic changes on the biological and neutralization sensitivity of the virus is unknown. The current study aims to characterize the genetic, biological, and neutralization sensitivity of HIV-1 identified in China between 2004 and 2007. Based on a total of 107 full-length envelope genes obtained directly from the infected patients, we found that those viruses fell into three major genetic groups: CRF01_AE, subtype B', and subtype C/CRF07_BC/CRF08_BC/B'C. Pseudotyped viruses built upon the viable env genes have demonstrated their substantial variability in mediating viral entry and in sensitivity to neutralization by subtype-specific plasma pools and broadly neutralizing monoclonal antibodies (bnmAb). Many viruses are resistant to one or more bnmAb, including those known to have high potency against diverse viruses from outside China. Sequence and structural analysis has revealed several mechanisms by which these resistant viruses escape recognition from bnmAb. We believe that these results will help us to better understand the impact of genetic diversity on the neutralizing sensitivity of the viruses and to facilitate the design of immunogens capable of eliciting antibodies with potency and breadth similar to those of bnmAb.

Broad neutralizing antibody response and genetic variation in HIV-1 env genes in Koreans with primary HIV-1 infections

To determine the neutralization profiles induced by HIV-1 Korean clade B, which has a monophyletic lineage and relative limited genetic diversity, we investigated the ability of HIV variants to elicit neutralizing antibodies in the immune response to primary infection. We selected seven Korean drug-naïve subjects with an HIV-1 primary infection and did pseudovirion-based neutralization assays using env genes of Korean HIV origin. The neutralizing antibody responses to the Korean clade B showed broad reactivity to subtype B but a highly subtype-specific pattern. The lengths of the amino acid sequences and the PNGS numbers in the V1-V5 region were positively correlated with neutralization. These results imply that the genetic characteristics of HIV-1 env may affect neutralizing antibody responses in HIV-1-infected individuals. This is the first report describing the relationship between neutralizing antibody responses and HIV-1 genetic characteristics in Korean subjects. It can be useful for developing AIDS vaccines against HIV-1 subtype B strains.

The effect of human immunodeficiency virus type 1 (HIV-1) gp41 variability on antibody detection

To determine whether genetic variability influences the ability to detect antibody, nine gp41 ectodomain recombinant proteins from human immunodeficiency virus type 1 (HIV-1) CRF07_BC, CRF01_AE and subtype B' were expressed in a bacterial expression system and purified. An indirect sandwich ELISA was developed with individual purified recombinant proteins. Plasma samples from 26 individuals infected with HIV-1 of different subtypes and four samples from the 1st international antibody reference panel were tested against each recombinant protein by ELISA. Heat-map and two-dimensional hierarchical clustering methods revealed that ELISA reactivity against antigens derived from the same subtypes clustered together. This suggests a similar reactivity pattern among infections of the same subtype, and thus the antigenicity of gp41 recombinant proteins may vary depending on the subtype, and subtype-related serotypes may exist among these antigens. Using association analysis methods, eight signature sites related to the subtype-specific reactivity patterns were identified. This study provides valuable information for the development of diagnostic assays with the ability to detect broadly cross-reactive antibodies induced by infection with different HIV-1 subtypes.

Genotypic and phenotypic characterization of HIV-1 CRF01_AE env molecular clones from infections in China

BACKGROUND

Although a great number of HIV-1 pseudoviruses have been generated for neutralization assays, circulating recombinant forms, such as CRF01_AE, are not included. Given the increasing prevalence of CRF01_AE, the establishment of a pool of CRF01_AE env isolates for the evaluation of potential HIV vaccines is needed.

MATERIALS AND METHODS

Full-length env genes were cloned from HIV-1 CRF01_AE-infected plasma samples collected in China and used to establish Env-pseudotyped viruses. The neutralization phenotypes of the pseudoviruses were characterized by testing against broadly neutralizing monoclonal antibodies, coreceptor antagonists, and 42 plasma samples that include 3 main prevalent HIV-1 subtypes in China.

RESULTS

Thirty-four genetically distinct CRF01_AE env genes were cloned and used to generate pseudotyped viruses. Of the 34 pseudoviruses, 32 used CCR5 as a coreceptor and 2 used CXCR4. The majority of pseudoviruses were resistant to the neutralizing antibodies IgG1b12 and 2G12 and susceptible to 2F5 and 4E10. There was significant variation of the neutralization susceptibility of pseudoviruses against 42 HIV-1-positive plasma samples. Based on their overall neutralization susceptibilities, the 34 CRF01_AE pseudoviruses were classified into 3 tiers: high, medium, and low.

CONCLUSION

The CRF01_AE pseudovirus isolates should be included in the panel of pseudoviruses used to assess vaccine-elicited neutralizing antibodies.

Drug resistance differences among HIV types and subtypes: a growing problem

Although HIV-1 subtype B accounts for only 10% of worldwide HIV infections, almost all knowledge regarding antiretroviral (ARV) drug development and viral resistance is based on this subtype. More recently, an increasing body of evidence suggests that distinct HIV genetic variants possess different biological properties, including susceptibility and response to ARVs. In this review, we will summarize recent in vitro and in vivo studies reporting such differences. In general terms, infections with most HIV variants respond well to ARVs, but minor differences in susceptibility, in the emergence and selection of subtype-specific drug resistance mutations and in the acquisition of similar mutations over the period of ARV exposure have been reported. Such differences impact on drugresistance interpretation algorithms, which are mostly based on inference from sequence information. Despite the differences observed, clinical response to ARV therapy among subjects infected with distinct HIV variants is effective, and the dissemination of ARV access in developing countries where non-B subtypes prevail should not be delayed.