Major histocompatibility complex class I-restricted cytotoxic T lymphocyte responses during primary simian immunodeficiency virus infection in Burmese rhesus macaques

Major histocompatibility complex class I (MHC-I)-restricted CD8(+) cytotoxic T lymphocyte (CTL) responses are crucial for the control of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) replication. In particular, Gag-specific CTL responses have been shown to exert strong suppressive pressure on HIV/SIV replication. Additionally, association of Vif-specific CTL frequencies with in vitro anti-SIV efficacy has been suggested recently. Host MHC-I genotypes could affect the immunodominance patterns of these potent CTL responses. Here, Gag- and Vif-specific CTL responses during primary SIVmac239 infection were examined in three groups of Burmese rhesus macaques, each group having a different MHC-I haplotype. The first group of four macaques, which possessed the MHC-I haplotype 90-010-Ie, did not show Gag- or Vif-specific CTL responses. However, Nef-specific CTL responses were elicited, suggesting that primary SIV infection does not induce predominant CTL responses specific for Gag/Vif epitopes restricted by 90-010-Ie-derived MHC-I molecules. In contrast, Gag- and Vif-specific CTL responses were induced in the second group of two 89-075-Iw-positive animals and the third group of two 91-010-Is-positive animals. Considering the potential of prophylactic vaccination to affect CTL immunodominance post-viral exposure, these groups of macaques would be useful for evaluation of vaccine antigen-specific CTL efficacy against SIV infection.     

Dynamics of Simian immunodeficiency virus-specific cytotoxic T-cell responses in tissues

Although the dynamics of human immunodeficiency virus and Simian immunodeficiency virus (SIV)-specific cytotoxic T cells (CTLs) have been well documented in the blood, little is known regarding CTL development in other tissues. In this study, seven Mamu-A*01+ macaques were inoculated with SIVmac. Two macaques were killed at 21 days of infection, and SIV gag p11C tetramer responses were measured in the blood, axillary and mesenteric lymph nodes, spleen, bone marrow, and thymus. Three with clinical signs of disease were killed and similarly examined. Four macaques were followed throughout disease progression, and intestinal biopsies and blood were examined at regular time points after inoculation. In animals followed prospectively, peak early tetramer responses were detected in the blood (3.9-19% of CD3+ CD8+ T cells) between day 14-21 post-inoculation (p.i.). After day 49, tetramer responses in the blood diminished and remained relatively stable through day 200, ranging from 0.7-6.5% of CD3+ CD8+ T cells. In contrast, tetramer-positive T cells increased in the intestine in later stages of infection (100-200 days p.i.) in all four infected animals (peak values from 5.3 to 28.8%). Percentages of tetramer-positive cells were consistently higher in the intestine than in the blood in all four animals after day 100. In animals with acquired immunodeficiency syndrome, percentages of CTL in tissues were variable, but were consistently higher in the intestine and spleen compared with blood. These data suggest that while high CTL responses develop at a similar rate, and magnitude in both peripheral and mucosal lymphoid tissues in primary SIV infection, mucosal CTL responses may predominate later in the course of the disease.     

Relative contribution of free-virus and synaptic transmission to the spread of HIV-1 through target cell populations

Human immunodeficiency virus can spread through target cells by transmission of cell-free virus or directly from cell-to-cell via formation of virological synapses. Although cell-to-cell transmission has been described as much more efficient than cell-free infection, the relative contribution of the two transmission pathways to virus growth during multiple rounds of replication remains poorly defined. Here, we fit a mathematical model to previously published and newly generated in vitro data, and determine that free-virus and synaptic transmission contribute approximately equally to the growth of the virus population.     

Differential selection in HIV-1 gp120 between subtype B and East Asianvariant B’

HIV-1 evolves strongly and undergoes geographic differentiation as it spreads in diverse host populations around the world.For instance,distinct genomic backgrounds can be observed between the pandemic subtype B,prevalent in Europe and North-America,and its offspring clade B' in East Asia.Here we ask whether this differentiation affects the selection pressure experienced by the virus.To answer this question we evaluate selection pressure on the HIV-1 envelope protein gp120at the level of individual codons using a simple and fast estimation method based on the ratio k_alk_s of amino acid changes to synonymous changes.To validate the approach we compare results to those from a state-of-the-art mixed-effect method.The agreement is acceptable,but the analysis also demonstrates some limitations of the simpler approach.Further,we find similar distributions of codons under stabilizing and directional selection pressure in gp120 for subtypes B and B' with more directional selection pressure in variable loops and more stabilizing selection in the constant regions.Focusing on codons with increased k_alk_s values in B',we show that these codons are scattered over the whole of gp120,with remarkable clusters of higher density in regions flanking the variable loops.We identify a significant statistical association of glycosylation sites and codons with increased k_alk_s values.     

Epistasis among Deleterious Mutations in the HIV-1 Protease

A central goal in molecular evolution is to understand how genetic interactions between protein mutations shape protein function and fitness. While intergenic epistasis has been extensively explored in eukaryotes, bacteria, and viruses, intragenic epistatic interactions have been insufficiently studied. Here, we employ a model system in which lambda phage fitness correlates with the enzymatic activity of human immunodeficiency virus type 1 (HIV-1) protease to systematically determine the epistatic interactions between intragenic pairs of deleterious protein substitutions. We generated 114 genotypes of the HIV-1 protease, each carrying pairs of nucleotide substitution mutations whose separated and combined deleterious effects on fitness were then determined. A high proportion (39%) of pairs displayed lethality. Several pairs exhibited significant interactions for fitness, including positive and negative epistasis. Significant negative epistatic interactions predominated (15%) over positive interactions (2%). However, the average ± SD epistatic effect, ē = 0.0025 ± 0.1334, was not significantly different from zero (p = 0.8368). Notably, epistatic interactions, regardless of epistatic direction, tend to be more frequent in the context of less deleterious mutations. In the present study, the high frequencies of lethality and negative epistasis indicate that the HIV-1 protease is highly sensitive to the effects of deleterious mutations. Therefore, proteins may not be as robust to mutational change as is usually expected.     

Preferential CTL targeting of Gag is associated with relative viral control in long-term surviving HIV-1 infected former plasma donors from China

It is generally believed that CD8⁺ cytotoxic T lymphocytes (CTLs) play a critical role in limiting the replication of human immunodeficiency virus type 1 (HIV-1) and in determining the outcome of the infection, and this effect may partly depend on which HIV product is preferentially targeted. To address the correlation between HIV-1-specific CTL responses and virus replication in a cohort of former plasma donors (FPDs), 143 antiretroviral therapy naive FPDs infected with HIV-1 clade B'' strains were assessed for HIV-1-specific CTL responses with an IFN-γ Elispot assay at single peptide level by using overlapping peptides (OLPs) covering the whole consensus clade B proteome. By using a Spearman''s rank correlation analysis, we found that the proportion of Gag-specific CTL responses among the total virus-specific CTL activity was inversely correlated with viral loads while being positively correlated to CD4 counts, as opposed to Pol- and Env-specific responses that were associated with increased viral loads and decreased CD4 counts. In addition, Vpr-specifc CTL responses showed a similar protective effect with Gag responses, but with a much lower frequency of recognition. Significantly, we also observed an association between HLA-A^*30/B^*13/Cw^*06 haplotype and lower viral loads that was probably due to restricted Gag-specific CTL responses. Thus, our data demonstrate the prominent role of Gag-specific CTL responses in disease control. The advantage of HLA-A^*30/B^*13/Cw^*06 haplotype in viral control may be associated with the contribution of Gag-specific CTL responses in the studied individuals.     

Differential selection in HIV-1 gp120 between subtype B and East Asian variant B’

HIV-1 evolves strongly and undergoes geographic differentiation as it spreads in diverse host populations around the world. For instance, distinct genomic backgrounds can be observed between the pandemic subtype B, prevalent in Europe and North-America, and its offspring clade B’ in East Asia. Here we ask whether this differentiation affects the selection pressure experienced by the virus. To answer this question we evaluate selection pressure on the HIV-1 envelope protein gp120 at the level of individual codons using a simple and fast estimation method based on the ratio k _a /k _s of amino acid changes to synonymous changes. To validate the approach we compare results to those from a state-of-the-art mixed-effect method. The agreement is acceptable, but the analysis also demonstrates some limitations of the simpler approach. Further, we find similar distributions of codons under stabilizing and directional selection pressure in gp120 for subtypes B and B’ with more directional selection pressure in variable loops and more stabilizing selection in the constant regions. Focusing on codons with increased k _a /k _s values in B’, we show that these codons are scattered over the whole of gp120, with remarkable clusters of higher density in regions flanking the variable loops. We identify a significant statistical association of glycosylation sites and codons with increased k _a /k _s values.     

含HIV-1 gag、gagV3基因的重组腺病毒伴随病毒的构建及其免疫原性的研究

将HIV－1中国株42（B亚型）gag基因及gag与gp120 V3区的嵌合基因gag V3插入腺病毒伴随病毒（AAV）表达载体（pSNAV）质粒中,构建重组质粒pSNAV-gag及pSNAV-gagV3;采用脂质体转染的方法分别将重组质粒转入BHK细胞,G418筛选得到转入重组质粒并能表达外源基因的细胞系,命名为BHK－gag及BHK－gagV3。用具有重组腺病毒伴随病毒（rAAV）包装功能的一种重组单纯疱疹病毒（rHSV）分析感染这两株细胞系,纯化后得到rAAV,电镜观察可见到大量实心病毒颗粒,核酸杂交检测重组病毒滴度达到10^12病毒颗粒／ml,重组病毒感染293细胞,ELISA检测有gag及gagV3基因的表达。用重组病毒免疫Balb/C小鼠,检测抗体及细胞免疫水平,证明重组病毒可以在小鼠体内诱导产生细胞及体液免疫。     

柳州和南宁HIV-1亚型分布及耐药情况调查

为了解柳州和南宁两市HIV-1亚型分布和耐药情况,在柳州和南宁招募HIV感染者和AIDS患者共304名,采集外周静脉血,从血浆中提取HIVRNA,扩增HIVpol基因并测序。将获得的序列进行系统进化树分析,结果表明柳州的HIV-1毒株中存在CRF01_AE和CRF07_BC两种亚型,其中CRF01_AE毒株占75.2%,CRF07_BC毒株占24.8%;南宁的HIV-1毒株中存在CRF01_AE、CRF08_BC、B亚型和C亚型共4种亚型,其中CRF01_AE和CRF08_BC仍是南宁最主要的亚型,CRF01_AE占85.8%,CRF08_BC占11.5%。根据所得的序列资料进行HIV-1耐药性分析,计算耐药率。计算结果表明,柳州未治疗和治疗研究对象的耐药率分别为3.3%和8.7%,南宁未治疗和治疗研究对象的耐药率分别为1.4%和27.5%。     

上海地区人类免疫缺陷病毒1型感染/艾滋病患者病毒耐药基因突变及亚型分布

目的 研究上海地区人类免疫缺陷病毒1型(HIV-1)感染／艾滋病(AIDS)患者中HIV-1耐药株出现的情况及亚型分布。方法 对33例HIV-1感染／AIDS患者的血浆HIV-1分离株,进行抗HIV-1药物(核苷类反转录酶抑制剂、非核苷类反转录酶抑制剂和蛋白酶抑制剂)的基因型耐药检测和亚型分析。结果 33例的HIV-1均未检出对PI的耐药突变;10例高效抗反转录病毒疗法(HAART)治疗失败或抑制病毒复制不完全者中,检出的耐药突变为70％,过渡型耐药突变为20％;23例未经抗HIV-1治疗者中,耐药突变为4．3％,过渡型耐药突变为13％。所有过渡型耐药突变均为T215S。15例经血制品传播的HIV- 1均为B亚型;18例经吸毒和性传播的HIV-1中,B和CRF01-AE亚型分别为39％,和33％,此外,还有C、D、G、K和CRF02-AG亚型。结论 上海地区HIV-1感染／AIDS患者中,HAART治疗失败或复制抑制不完全者HIV-1的NRTI和NNRTI耐药突变率高;吸毒和性传播者的HIV-1中,除主要为B和CRF01-AE亚型外,尚有其他少见的亚型。     

The evolution of HIV-1 and the origin of AIDS

The major cause of acquired immune deficiency syndrome (AIDS) is human immunodeficiency virus type 1 (HIV-1). We have been using evolutionary comparisons to trace (i) the origin(s) of HIV-1 and (ii) the origin(s) of AIDS. The closest relatives of HIV-1 are simian immunodeficiency viruses (SIVs) infecting wild-living chimpanzees (Pan troglodytes troglodytes) and gorillas (Gorilla gorilla gorilla) in west central Africa. Phylogenetic analyses have revealed the origins of HIV-1: chimpanzees were the original hosts of this clade of viruses; four lineages of HIV-1 have arisen by independent cross-species transmissions to humans and one or two of those transmissions may have been via gorillas. However, SIVs are primarily monkey viruses: more than 40 species of African monkeys are infected with their own, species-specific, SIV and in at least some host species, the infection seems non-pathogenic. Chimpanzees acquired from monkeys two distinct forms of SIVs that recombined to produce a virus with a unique genome structure. We have found that SIV infection causes CD4⁺ T-cell depletion and increases mortality in wild chimpanzees, and so the origin of AIDS is more ancient than the origin of HIV-1. Tracing the genetic changes that occurred as monkey viruses adapted to infect first chimpanzees and then humans may provide insights into the causes of the pathogenicity of these viruses.     

Accessory Mutations Maintain Stability in Drug-Resistant HIV-1 Protease

The underlying mechanisms driving the evolution of drug resistance in human immunodeficiency virus (HIV) are only partially understood. We investigated the evolutionary cost of the major resistance mutations in HIV-1 protease in terms of protein stability. The accumulation of resistance mutations destabilizes the protease, limiting further adaptation. From an analysis of clinical isolates, we identified specific accessory mutations that were able to restore the stability of the protease or even increase it beyond the wild-type baseline. Resistance mutations were also found to decrease the activity of HIV protease near neutral pH values, while incorporating stabilizing mutations improved the enzyme's pH tolerance. These findings help us to explain the prevalence of mutations located far from the active site and underscore the importance of protein stability during the evolution of drug resistance in HIV.     

Roles of the interactions between Env and Gag proteins in the HIV-1 replication cycle

The Env and Gag proteins of HIV-1 are the two major structural proteins of this retrovirus. The interactions between Env and Gag proteins and their regulation in HIV-1 are required for several steps of the replication cycle, involving not only virus assembly, specifically Env incorporation, but also entry steps after virus maturation. A large number of host factors and certain membrane microdomains appear to engage both in transport/trafficking of Env and/or Gag proteins, and in the interactions of these two proteins. The present review briefly summarizes our current knowledge regarding the roles of the interactions between Env and Gag proteins in the virus replication cycle.     

Effects of neutralizing antibodies on escape from CD8+ T-cell responses in HIV-1 infection

Despite substantial advances in our knowledge of immune responses against HIV-1 and of its evolution within the host, it remains unclear why control of the virus eventually breaks down. Here, we present a new theoretical framework for the infection dynamics of HIV-1 that combines antibody and CD8⁺ T-cell responses, notably taking into account their different lifespans. Several apparent paradoxes in HIV pathogenesis and genetics of host susceptibility can be reconciled within this framework by assigning a crucial role to antibody responses in the control of viraemia. We argue that, although escape from or progressive loss of quality of CD8⁺ T-cell responses can accelerate disease progression, the underlying cause of the breakdown of virus control is the loss of antibody induction due to depletion of CD4⁺ T cells. Furthermore, strong antibody responses can prevent CD8⁺ T-cell escape from occurring for an extended period, even in the presence of highly efficacious CD8⁺ T-cell responses.     

Inhibition of HIV-1 integrase by modified oligonucleotides: Optimization of the inhibitor structure

Integration of human immunodeficiency virus type 1 DNA into the infected cell genome is one of the key steps of the viral replication cycle. Therefore, viral integrase is of interest as a target for new antiviral drugs. Conjugates of 11-mer single-stranded oligonucleotides with hydrophobic molecules were shown to be efficient integrase inhibitors, inducing dissociation of the integrase-viral DNA complex. The dependence of the conjugate inhibitory activity on the oligonucleotide length and structure as well as on the structure of hydrophobic molecules was studied. Conjugates with eosin and oleic acid proved to be the most active. Conjugates of these molecules with 2′-O-methyl-oligonucleotide inhibited integrase at concentrations 50–100 nM but did not influence some other DNA-binding enzymes.     

人体黏膜活组织模型在HIV-1 性传播途径感染中的应用

性传播途径已经成为全球人免疫缺陷病毒1型 (Human immunodeficiency virus type 1,HIV-1) 传播的主要方式。对HIV-1黏膜感染机制的深入理解,将有助于研发新型有效的生物技术阻断其感染和传播。目前,HIV-1黏膜感染机制的研究主要依赖于体外细胞培养和灵长类动物模型。近年来,一种新型黏膜活组织模型 (包括人体生殖道或肠道黏膜等组织) 的建立,可再现HIV-1突破黏膜屏障进入基底侧的生物学过程,适用于HIV-1黏膜感染机制与黏膜局部感染阻断生物技术的临床前有效性评价研究。