Blinded, multicenter quality control study for the quantification of human immunodeficiency virus type 1 RNA in plasma by the Belgian AIDS reference laboratories

Objective   In order to evaluate the interlaboratory variation of HIV-1 RNA measurements in plasma, the Belgian AIDS reference laboratories organized a blinded multicenter quality control study.
Methods   Atest panel of coded spiked HIV-1 plasma samples reflecting the dynamic range of the assay was composed and distributed. The HIV-1 RNA concentration of these samples was determined by the eight Belgian AIDS reference laboratories by means of the Amplicor HIV-1 Monitor version 1.5 assay.
Results   Analysis of the results demonstrated that there was little interlaboratory variation for the high concentration range (4.0-5.7 log₁₀ copies/mL), never exceeding 0.2 log₁₀ copies/mL. However the standard deviation for the low concentration range (2.6-3.9 log₁₀ copies/mL) reached up to 0.22 log₁₀ copies/mL.
Conclusions   Since interlaboratory variability never reached 0.5 log₁₀ copies/mL and each of the laboratories was able to detect four-fold differences in plasma HIV-1 RNA levels, the Amplicor assay can be used in multicenter studies without a centralized analysis of samples. Furthermore, this well-characterized proficiency panel of spiked plasma samples could be used as a standard in the study of interassay comparisons.     

Serum antibody pattern, antigenemia, and virus isolation in infants born to mothers seropositive for human immunodeficiency virus type 1

Forty children born to mothers seropositive for the human immunodeficiency virus type 1 (HIV-1) followed-up to 15 months after birth were studied by means of serum antibody patterns to individual viral polypeptides, by the presence of detectable levels of viral core antigen (p24) and virus in serum and peripheral blood lymphocytes, and by total lymphocyte counts and T4/T8 lymphocyte ratios. The results obtained indicate that a persistent antigenemia is significantly associated with positive virus isolation from peripheral blood lymphocytes and with changes in the intensity of antibody reaction to core (p24, p17) and pol (p31) antigens. Six children (15%) presented unequivocal signs of HIV-1 infection and five also had signs of immune system involvement.     

Low risk of transmission of the human immunodeficiency virus by a solvent-detergent-treated commercial factor VIII concentrate.

A study evaluating the risk of a commercial factor VIII (FVIII) concentrate's transmitting the human immunodeficiency virus (HIV) was carried out on hemophiliacs, by using multiple serological markers and the polymerase chain reaction (PCR). Twenty-nine hemophiliacs, negative for HIV antibodies, were treated for 18 months with a concentrate that had been inactivated by solvent-detergent. HIV-1 antibodies and antigen were assayed during the follow-up period. At the end of the study, all patients were also tested by the HIV 1 + 2 combined antibody assay; Western blot (WB) antibody analysis; and in eight cases, by an HIV-1 PCR technique. Patients received a yearly median FVIII dose of 35,330 IU (range 3,300-306,000); the median number of lots given to each patient was 6 (1-45). During the follow-up period and at the end of the study, HIV-1 antibodies and antigen were not detected in any of the subjects. The HIV 1 + 2 combined assay and WB analysis carried out only at the end of the study were negative. HIV-1 PCR was negative in all the tested patients. This study has shown that this solvent-detergent-treated FVIII concentrate did not transmit HIV.     

使用多重巢式PCR对我国HIV-1主要流行株亚型鉴定方法的建立

目的 建立一套新的亚型鉴定方法，仅仅使用巢式PCR，一次扩增，即可对我国HIV-1主要流行株B、C和CRF01-AE进行亚型鉴定。方法 从HIV阳性样本中提取核酸，使用能覆盖HIV-1型M组gag区的引物进行第一轮扩增，第二轮扩增则使用分别检测B、C、CRF01-AE亚型的三套特异性引物进行扩增，三套引物放在同一个反应管中。反应产物经琼脂糖电泳后观察，不同亚型的位置不同，以此来判断亚型。另外设计一套引物，专门检测我国重组株CRF07-BC和CRF08-BC。所有样品均经过基因测序、系统进化树分析，以进行结果验证。结果 在检测的119份样品中，经基因测序和系统进化树分析证实B亚型样品43份(欧美B11份，泰国B32份)，C、CRF01-AE、A和D亚型样品分别为54份、17份、3份和2份。其中C亚型的样品，有52份属于CRF07-BC和CRF08-BC。而经过上述多重巢式PCR方法检测到的B亚型样品为35份(81．4％)，C亚型46份(85．2％)和CRF01-AE13份(76．5％)。另外，检测CRF07-BC和CRF08-BC重组株的引物特异性地检测到43份(82．7％)样品。上述结果与基因分析结果吻合，各个亚型之间无交叉，一种亚型的特异性引物只对该亚型有反应，而对其他亚型无反应，特异性达到100％。虽然有时会有非特异扩增带，但一般不影响结果判断。结论 我们建立了一套简单快速的H1V-1亚型鉴定方法，不需基因测序，即可检测我国主要流行株B、C、CRF01-AE、CRF07-BC和CRF08-BC。该方法具有高度特异性和敏感性，可以作为初筛方法在我国及其他国家HIV-1实验室推广使用。     

Molecular clock-like evolution of human immunodeficiency virus type 1

The molecular clock hypothesis states that the rate of nucleotide substitution per generation is constant across lineages. If generation times were equal across lineages, samples obtained at the same calendar time would have experienced the same number of generations since their common ancestor. However, if sequences are not derived from contemporaneous samples, differences in the number of generations may be misinterpreted as variation in substitution rates and hence may lead to false rejection of the molecular clock hypothesis. A recent study has called into doubt the validity of clock-like evolution for HIV-1, using molecular sequences derived from noncontemporaneous samples. However, after separating their within-individual data according to sampling time, we found that what appeared to be nonclock-like behavior could be attributed, in most cases, to noncontemporaneous sampling, with contributions also likely to derive from recombination. Natural selection alone did not appear to obscure the clock-like evolution of HIV-1.     

Nested polymerase chain reaction for detection of human immunodeficiency virus type 1 DNA in clinical specimens.

A highly sensitive two-step polymerase chain reaction (PCR) method was evaluated for detection of human immunodeficiency virus type 1 (HIV-1) DNA in clinical specimens. The product resulting from the first amplification reaction is used as the template for the second PCR with an internal (nested) primer pair. Even when starting from a single copy of HIV-1 DNA, the double PCR product was readily detected by direct visualization in ethidium bromide-stained agarose gels. Amplification of minute amounts of HIV-1 DNA was successful in a considerable excess of HIV-1 negative DNA than reported previously. All of 85 HIV-1-infected individuals were PCR-positive with at least two of the three sets of primers used, 252 of 255 amplifications allowing unambiguous visualization of a unique DNA fragment of the expected size. The two-step amplification protocol is simple and rapid and fulfills the requirements of sensitivity and specificity for use in a clinical laboratory.     

Perinatal infection by human immunodeficiency virus type 1 (HIV-1): relationship between proviral copy number in vivo, viral properties in vitro, and clinical outcome.

Human immunodeficiency virus type 1 (HIV-1) isolates from 25 perinatally HIV-1 infected children were classified according to their capacity to replicate in vitro as rapid (R), intermediate (S/R) and slow (S) variants. R-type viruses replicated on peripheral blood mononuclear cells (PBMCs) and grew better in T-lymphoid cells, even though 9 out of 12 isolates also maintained tropism for monocytoid cells. The S/R-type isolates replicated efficiently after several days of culture, while the S-type viruses displayed only a low and transient replication activity; however, both S/R- and S-type isolates exerted viral transactivation activity in an indicator monocytoid cell line. Replication patterns in vitro were significantly associated in vivo with the number of HIV-1 copies in PBMCs as determined by polymerase chain reaction: in children with R-type isolates, the number of HIV-1 proviral DNA molecules/10(5) PBMCs ranged from 62 to 571, and in children with S/R and S isolates the range was 5-43. Seven children had severe symptomatic HIV-1 infection, and in all an R-type virus was identified; 18 children had no or only mild symptoms, and among these, S-, S/R-, and R-type isolates were found in 5, 8, and 5 cases, respectively. Besides demonstrating HIV-1 variability in perinatal infection, these findings suggest that R-type virus might be a prerequisite for disease progression.     

HIV-1 Gag、Tat、Rev和Nef蛋白特异性的免疫应答

目的：探讨中国HIV／AIDS患者HIV—1 Gag、Tat、Rev和Nef蛋白特异性CTL应答的特征。方法：应用覆盖HIV-1 B、C亚型Gag、Tat、Rev和Nef蛋白的220个肽段作为抗原，通过ELISPOT方法俭测HIV／AIDS患者HIV特异性CTL应答。结果：无沦HIV—1 B亚型还是HIV-1C亚型所构建肽库的应答强度和频率，主要集中在Gag和Nef蛋白，Tat和Rev蛋白也有不同程度的应答。HIV—1 B、C亚型间应答比较，整体应答强度大致相同，但免疫优势区间存在着一定的差异，B亚型Gagp24亚蛋白的288～313氨基酸区应答最强，而C亚型Gagp24亚蛋白的155～181氨基酸区应答最强；两个亚型免疫优势区应答频率最高的都是Nef蛋白106～143氨基酸区(48．1％)。结论：中国人群CTL应答多集中在Gag和Nef蛋白，B、C业型间略有差异且存在交叉识别，这对设计针对中国人群的HIV疫苗是有重要的意义。     

人免疫缺陷病毒1型CRF07_BC毒株准种间的重组

目的 通过研究人类免疫缺陷病毒1型（human immunodeficiency virus1，HIV-1）感染者个体内准种间的差异，探讨HIV的系统进化的发生模式。方法 从HIV-1感染者血浆中提取总RNA，通过逆转录多聚酶链反应（RT-PCR）获得HIV．1gp120全长基因，纯化后装入T载体，转化至TOP10大肠埃希菌内增殖，通过蓝白斑筛选获得阳性克隆，对所获得的目的克隆测序并分析。结果 获得同一患者的16个克隆的gp120全长基因序列，通过系统进化树分析，克隆序列均为CRF07_BC亚型，但在系统进化树上16个克隆可明显分为A、B两群，其中13个克隆属于A群，2个克隆属于B群，1个克隆（编号XPD7）位于A、B群之间，通过simplot软件的重组分析，发现XPD7克隆为A群和B群的重组株。结论 发现了我国广泛流行的HIV-1CRF07-BC毒株准种间的重组现象，准种间的重组作为HIV进化的一种有效手段将导致HIV毒株的快速进化的发生，可能更易逃脱宿主的免疫监控。     

Long-term survival and virus production in human primary macrophages infected by human immunodeficiency virus

The role of macrophages in the pathogenesis and progression of human immunodeficiency virus (HIV)-related infection is substantiated by in vitro and in vivo evidence. The unique ability to survive HIV infection and produce viral particles for long periods is postulated. Detailed studies of this phenomenon are lacking. The dynamics of HIV-1 replication and cumulative virus production was studied in long-term cultures of macrophages in the presence or in the absence of antiviral drugs. Multiply spliced and unspliced HIV-RNA production was assessed by quantitative PCR, and the number of infected cells was monitored by FACS analysis. Cumulative HIV-1 production was determined by a trapezoidal equation, including such parameters as times of collection and experimental values of genomic-RNA and p24 gag antigen. Unspliced and multiply spliced HIV-RNA increased linearly after macrophage infection; reached levels of 1.5 x 10(8) and 2.8 x 10(5) copies/10(5) cells, respectively, at day 10; and then remained stable throughout the course of the experiment. Cumulative production of genomic-RNA and p24 gag antigen was 10(10) copies/10(6) cells and 10(7) pg/10(6) cells, respectively, with an average of >200 virus particles produced daily by each macrophage. AZT decreased the cumulative production of both genomic-RNA and p24 gag antigen down to 2.5 x 10(9) copies and 1.1 x 10(6) pg/10(6) cells (73.8% and 88.9% inhibition, respectively) up to day 50 without virus breakthrough. Ritonavir had a limited, but consistent, efficacy on the release of mature virus proteins (about 40% inhibition), but not on HIV-RNA production. In conclusion, the long-term dynamics and the high cumulative virus production that characterize HIV-1 infection of macrophages underscore the peculiar role of these cells as a persistently infected reservoir of HIV.     

Human immunodeficiency virus type 1 fitness and tropism: concept,quantification, and clinical relevance

Two distinct aspects of human immunodeficiency virus type 1 (HIV-1) biopathology with important implications for the management of treated patients have emerged during the last decade: changes in relative viral fitness, and viral tropism. First, it has been observed that HIV-1 accumulates deleterious mutations leading to drug resistance and different degrees of reduction in relative fitness during antiretroviral therapy (ART). Although the latter normally parallel a failure of ART resulting from selection of resistant mutants, the drop in viral replication capacity may be beneficial for the host. Moreover, specific antiviral compounds aimed at reducing viral fitness could be developed. Analysis of the determinants of viral fitness in highly evolving viral populations has shown that viral extinction may also be obtained by forcing highly dynamic viral populations through increased (lethal) mutagenesis that abolishes viral replication (violation of the error threshold). It could be of great interest in the near future to address this point with strategies specifically planned at the molecular level. Furthermore, diagnostic evaluation limited to the master sequence has low predictive value in rapidly evolving viral populations. These observations, together with the evidence that all of the methodologies currently used for fitness analysis have important limitations, strongly suggest that further research is warranted. This should use highly sensitive and flexible technologies to evaluate viral fitness directly in vivo or ex vivo, not only for the dominant mutants, but also for minority variants. Second, discovery of the two main co-receptors for HIV-1, CCR5 and CXCR4, has led to a better understanding of the interaction of the viral envelope with host cells and to the development of novel therapeutic agents that inhibit viral entry. In this perspective, analysis of HIV-1 tropism has acquired a major diagnostic role.     

Truncated forms of human and simian immunodeficiency virus in infected individuals and rhesus macaques are unique or rare quasispecies

Truncated proviruses of variable sizes are present in peripheral blood mononuclear cells (PBMC) of human immunodeficiency virus type 1 (HIV-1)-infected persons and simian immunodeficiency virus (SIV)-infected rhesus macaques. Here, we investigated whether the highly deleted HIV and SIV proviruses are present in infected organisms as multiple copies or whether each truncated provirus is unique. Using end-point dilution, multiple long-distance (LD) DNA PCR assays were run in parallel using DNA extracted from PBMC of seropositive, treatment-naive persons and from lymph nodes of a rhesus monkey inoculated with cloned, full-length SIVmac239 DNA. The PCR products were titrated and mapped. Most truncated proviruses were present in the DNA samples tested as single, nonintegrated molecules that differed from one another in size and/or nucleotide sequence. These results indicate that truncated primate lentiviral sequences found in infected tissues are unique or rare quasispecies that do not replicate significantly.     

Characterization of human T-cell lines harboring defective human immunodeficiency virus type 1

Defective HIV-producing T-cell lines were subcloned from MT-4/HIV_HTLV-IIIB MOLT-4/HIV_HTLV-IIIB, and H9/HIV_HTLV-IIIB cell lines chronically infected with HIV. The NY-M10 cell line derived from MOLT-4/HIV_HTLV-IIIB and the NY-H6 cell line derived from H9/HIV_HTLV-IIIB produce defective HIV, which lacks the ability to infect human T-cell lines. NY-M10 cells retain the capacity to form multinucleated giant cells in cocultivation with HIV-uninfected CD4-positive cells. However, NY-H6 cells failed to fuse with CD4-positive cells. Electron microscopic analysis indicated that the defective HIV produced from NY-M10, like those reported previously, lacked the structure of the nucleocapsid, and the virion released from NY-H6 was indistinguishable from those of authentic HIV particles. Southern and Northern blotting analyses of NY-M10 and NY-H6 cleared that the genome of those defective viruses was not significantly deleted, suggesting minor mutation(s) should take place on the viral genome.     

HIV-1整合酶蛋自(p31)的表达、纯化及其在血清学诊断中的应用

在大肠杆菌中，利用pET－3c表达载体，高效表达了具有全长序列的HIV—1整合酶蛋白（p31）。表达产物主要以包涵体的形式存在，用1mol／LNaCl溶解包涵体可部分地溶解p31蛋白，溶解上清中p31蛋白具有很高的纯度。本文进一步描述了一种在变性条件下重组蛋白的纯化方法，即将包涵体用8mol／L尿素溶解，先后经过S-SepharoseFastFlow与Sephacryl-300柱层析，可将重组产物纯化到电泳纯。纯化蛋白以1μg／ml包被ELISA板，分析正常人及HIV－1阳性个体的血清，结果重组p31与检测的所有41份阳性血清均可发生特异反应，而与36份正常血清则不起反应，表明纯化的重组蛋白可用于检测血清中的抗HIV-1抗体。     

CXCR4 tropic human immunodeficiency virus type 1 induces an apoptotic cascade in immature infected thymocytes that resembles thymocyte negative selection

HIV-1 often replicates in the thymus of infected individuals, causing thymocyte depletion and thymic dysfunction. Nevertheless, the mechanisms by which thymocyte depletion occurs are not clear. Here we report that HIV-1 infection induced apoptosis primarily in productively infected thymocytes; aldrithiol-2 or Efavirenz treatment largely abrogated HIV-1-induced apoptosis. Moreover, X4-HIV-1 induced apoptosis primarily in immature CD4+ CD8+ (DP) thymocytes whereas most mature CD4 or CD8 single-positive (SP) thymocytes were resistant to X4 HIV-1-induced apoptosis despite infection. Consistent with this, we observed significant induction of several genes involved in negative selection of DP thymocytes. Furthermore, treatment of thymocytes with cycloheximide abrogated HIV-1-induced apoptosis, implying a requirement for de novo protein synthesis. Our results suggest that HIV-1-induced apoptosis of thymocytes requires the activation of caspases and the participation of mitochondrial apoptosis effectors, which serve to amplify the apoptotic signal, a process similar to that elaborated during thymocyte negative selection.     

Half-genome human immunodeficiency virus type 1 constructs for rapid production of reporter viruses

The use of reporter constructs of HIV-1 molecular clones has been useful in studying the effects of infection on individual cells. A strategy of producing viral half-genome constructs containing reporter genes that can be used to produce recombinant complete infectious virions is described. This approach allows rapid generation of reporter and non-reporter virions from the same genetic construct, obviating the need to produce a new reporter genetic construct for each viral change to be studied. We provide an example of the utility of this system for studying the effects of Nef on infected cells.