Intrahost evolution of the HIV-2 capsid correlates with progression to AIDS

HIV-2 infection will progress to AIDS in most patients without treatment, albeit at approximately half the rate of HIV-1 infection. HIV-2 capsid (p26) amino acid polymorphisms are associated with lower viral loads and enhanced processing of T cell epitopes, which may lead to protective Gag-specific T cell responses common in slower progressors. Lower virus evolutionary rates, and positive selection on conserved residues in HIV-2 env have been associated with slower progression to AIDS. In this study we analysed 369 heterochronous HIV-2 p26 sequences from 12 participants with a median age of 30 years at enrolment. CD4% change over time was used to stratify participants into relative faster and slower progressor groups. We analysed p26 sequence diversity evolution, measured site-specific selection pressures and evolutionary rates, and determined if these evolutionary parameters were associated with progression status. Faster progressors had lower CD4% and faster CD4% decline rates. Median pairwise sequence diversity was higher in faster progressors (5.7x10-3 versus 1.4x10-3 base substitutions per site, P<0.001). p26 evolved under negative selection in both groups (dN/dS=0.12). Median virus evolutionary rates were higher in faster than slower progressors - synonymous rates: 4.6x10-3 vs. 2.3x10-3; and nonsynonymous rates: 6.9x10-4 vs. 2.7x10-4 substitutions/site/year, respectively. Virus evolutionary rates correlated negatively with CD4% change rates (ρ = -0.8, P=0.02), but not CD4% level. The signature amino acid at p26 positions 6, 12 and 119 differed between faster (6A, 12I, 119A) and slower (6G, 12V, 119P) progressors. These amino acid positions clustered near to the TRIM5α/p26 hexamer interface surface. p26 evolutionary rates were associated with progression to AIDS and were mostly driven by synonymous substitutions. Nonsynonymous evolutionary rates were an order of magnitude lower than synonymous rates, with limited amino acid sequence evolution over time within hosts. These results indicate HIV-2 p26 may be an attractive therapeutic target.

HIV treatment in Guinea-Bissau: room for improvement and time for new treatment options

Despite advances in the treatment quality of HIV throughout the world, several countries are still facing numerous obstacles in delivering HIV treatment at a sufficiently high quality, putting patients' lives in jeopardy. The aim of this status article is to give an overview of HIV treatment outcomes in the West African country, Guinea-Bissau, and to assess how newer treatment strategies such as long-acting injectable drugs or an HIV cure may limit or stop the HIV epidemic in this politically unstable and low-resource setting. Several HIV cohorts in Guinea-Bissau have been established and are used as platforms for epidemiological, virological, immunological and clinical studies often with a special focus on HIV-2, which is prevalent in the country. The Bandim Health Project, a demographic surveillance site, has performed epidemiological HIV surveys since 1987 among an urban population in the capital Bissau. The Police cohort, an occupational cohort of police officers, has enabled analyses of persons seroconverting with estimated times of seroconversion among HIV-1 and HIV-2-infected individuals, allowing incidence measurements while the Bissau HIV Cohort and a newer Nationwide HIV Cohort have provided clinical data on large numbers of HIV-infected patients. The HIV cohorts in Guinea-Bissau are unique platforms for research and represent real life in many African countries. Poor adherence, lack of HIV viral load measurements, inadequate laboratory facilities, high rates of loss to follow-up, mortality, treatment failure and resistance development, are just some of the challenges faced putting the goal of "90-90-90″ for Guinea-Bissau well out of reach by 2020. Maintaining undetectable viral loads on treatment as a prerequisite of a cure strategy seems not possible at the moment. Thinking beyond one-pill-once-a-day, long-acting antiretroviral treatment options such as injectable drugs or implants may be a better treatment option in settings like Guinea-Bissau and may even pave the way for an HIV cure. If the delivery of antiretroviral treatment in sub-Saharan Africa in a sustainable way for the future should be improved by focusing on existing treatment options or through focusing on new treatment options remains to be determined.

A17 The effect of intra-host evolution of HIV-2 capsid on disease progression

The human immunodeficiency virus type 2 (HIV-2) is an important cause of acquired immune deficiency syndrome (AIDS) in West Africa. The virus started circulating in humans around 1938 and has spread predominantly within West Africa with an estimated 1–2 million people being infected today. Compared with the pandemic HIV-1, HIV-2 infected people have longer AIDS-free survival times, higher CD4+ counts and lower risk of vertical and horizontal transmission. Approximately 35 per cent of HIV-2 infected individuals are classified as so-called long-term non-progressors with undetectable viral loads and limited disease progression after 10 years of follow-up. It has been shown that HIV-2 is more sensitive to the host restriction factor TRIM5α when compared with HIV-1, and this has been linked to conformational changes in the retroviral capsid. TRIM5α binds at the interface between three capsid hexamers, initiates early uncoating and proteasomal degradation. TRIM5 genotype has shown only modest effects on HIV-1 disease outcomes. HIV-2 capsid sequences bearing a specific poly-proline motif have been associated with lower viral loads and presentation of protective HLA I-restricted epitopes. The major aims of this study were to (1) determine HIV-2 capsid intra-host evolutionary rates and (2) identify residues that are affected by positive selection and that can be linked to HIV-2 viral load and disease progression in conjunction with TRIM5 genotype. The Guinea-Bissau Police cohort is unique, with decades of relatively frequent follow-up. One hundred and sixty-five patients were included for genotyping of TRIM5, 62 females and 103 males. Median age at enrolment was 52.6 years (range 30–87) and 7.9 per cent of patients had a CD4 percentage < 15 per cent at enrolment. Six of these individuals were included for amplification of HIV-2 capsid from longitudinally collected samples. Viral RNA was extracted from stored blood plasma samples and capsid of the circulating viral quasispecies was amplified, cloned, and sequenced, as previously described. Bayesian analysis will be used to determine intra-host evolutionary rates, dN/dS ratios and how these parameters associate with disease progression and TRIM5 genotype.

Is low-level HIV-1 viraemia associated with elevated levels of markers of immune activation, coagulation and cardiovascular disease?

OBJECTIVES

The clinical significance of low-level viraemia (LLV) during antiretroviral therapy (ART) is debated. We retrospectively investigated longitudinal levels of plasma markers associated with inflammation, altered coagulation and cardiovascular disease in Swedish HIV-positive adults in relation to LLV or permanent virological suppression during long-term ART.

METHODS

Plasma levels of C-reactive protein (CRP), D-dimer, vascular cell adhesion molecule 1 (VCAM-1), suppression of tumorigenicity 2 (ST2), growth differentiation factor 15 (GDF-15), soluble CD14 (sCD14), soluble CD163 (sCD163), interferon-γ-induced protein 10 (IP-10) and β-2-microglobulin were measured in 34 individuals with LLV (viral load 50-999 HIV-1 RNA copies/mL) and in matched controls with persistent virological suppression. Biomarker levels were analysed in samples obtained during episodes of LLV and follow-up samples obtained 1 year later (with similar timing for controls). All biomarkers were analysed using an independent sample t-test and analysis of covariance (ANCOVA) after logarithmic transformation. Log-rank analysis was applied for markers with concentration values out of range.

RESULTS

Compared with controls, patients with LLV had significantly higher levels of GDF-15 [geometric mean 3416 (95% confidence interval (CI) 804-14 516) pg/mL versus 2002 (95% CI 355-11 295) pg/mL in controls; P = 0.026] and D-dimer [mean 1114 (95% CI 125-9917) ng/mL versus 756 (95% CI 157-3626) ng/mL; P = 0.038] after adjustment for age, CD4 count nadir and type of ART. In the unadjusted t-test, only GDF-15 was significantly higher and in the log-rank test, both GDF-15 and D-dimer were significantly elevated. No significant differences were observed for the other biomarkers analysed.

CONCLUSIONS

Although levels of inflammation markers were similar in ART recipients with and without LLV, persons with LLV had significantly higher levels of GDF-15 and D-dimer. These findings suggest a potential link between LLV and cardiovascular outcomes.

Human immunodeficiency virus type 1 biological variation and coreceptor use: from concept to clinical significance

There is ample evidence for intra-patient evolution of the human immunodeficiency virus type 1 (HIV-1) biological phenotype during the pathogenic process. Evolution often involves switch of coreceptor use from CCR5 to CXCR4, but change to more flexible use of CCR5 occurs over time even in patients with maintained CCR5 use. The increasing use of entry inhibitors in the clinic, often specific for one or the other HIV-1 coreceptor or with different binding properties to CCR5, calls for virus testing in patients prior to treatment initiation. Cell lines expressing CCR5/CXCR4 chimeric receptors are tools for testing viruses for mode of CCR5 use. It is conceivable that small-molecule entry inhibitors that differentially bind to CCR5 can be matched for best effect against HIV-1 with different modes of CCR5 use, thereby allowing an individualized drug choice specifically tailored for each patient.

Gene expression profiling of human placentas from preeclamptic and normotensive pregnancies

The aim of this study was to investigate patterns of gene expression in placental samples from patients with preeclampsia (PE), persistent bilateral uterine artery notching (without PE), and normal controls. This study included placental tissue from nine women with PE, seven with uncomplicated pregnancies and five with bilateral uterine artery notching in Doppler velocimetry tracings. Human cDNA microarrays with 6500 transcripts/genes were used and the results verified with real-time PCR and in-situ hybridization. Multidimensional scaling method and random permutation technique demonstrated significant differences among the three groups examined. Within the 6.5K arrays, 6198 elements were unique cDNA clones representing 5952 unique UniGenes and 5695 unique LocusLinks. Multidimensional scaling plots showed 5000 genes that met our quality criteria; among these, 366 genes were significantly different in at least one comparison. Differences in three genes of interest were confirmed with real-time PCR and in-situ hybridization; acid phosphatase 5 was shown to be overexpressed in PE samples and calmodulin 2 and v-rel reticuloendotheliosis viral oncogene homolog A (RELA) were downregulated in PE and uterine artery notch placentas. In conclusion downregulation of RELA and calmodulin 2 might represent an attempt by the placenta to compensate for elevations in intracellular calcium, possibly caused by hypoxia and/or apoptosis, in both pregnancies with uterine artery notching and preeclampsia.

Impact of transposable elements on the evolution of mammalian gene regulation

Transposable elements (TEs) are present in all organisms and nearly half of the human and mouse genome is derived from ancient transpositions. This fact alone suggests that TEs have played a major role in genome organization and evolution. Studies undertaken over the last two decades or so clearly show that TEs of various kinds have played an important role in organism evolution. Here we review the impact TEs have on the evolution of gene regulation and gene function with an emphasis on humans. Understanding the mechanisms resulting in genomic change is central to our understanding of gene regulation, genetic disease and genome evolution. Full comprehension of these biological processes is not possible without an in depth knowledge of how TEs impact upon the genome.

Repetitive elements in the 5' untranslated region of a human zinc-finger gene modulate transcription and translation efficiency

A substantial proportion of the human genome consists of repetitive sequences. Although most of these sequences are nonessential for the organism, retroelements, such as Alu sequences, L1s, and HERVs (human endogenous retroviruses), have recently been implicated in the regulation of various genes. Our laboratory previously identified a novel, alternatively spliced zinc-finger gene, ZNF177, which incorporates Alu L1, and HERV segments into the 5' untranslated region (UTR) of transcripts. In this study, we investigated the genomic structure and functional significance of the repetitive sequences in the 5' UTR of ZNF177 mRNAs. Using luciferase and GFP reporter constructs, we assessed the effect of the HERV, Alu, and L1 sequences on gene expression levels. Our results indicate that the presence of the retroelement sequences, particularly the Alu and L1 segments which form one 5' UTR exon, modifies the expression level of both reporter genes. We present evidence that the Alu and L1 sequences alter both the RNA and protein levels of reporter genes by increasing transcription efficiency while decreasing translation efficiency. Our findings indicate that the Alu and L1 repeats in the 5' UTR of ZNF177 exert a positive transcriptional enhancer effect, but repress translation of the zinc finger gene. In addition, our analysis of a 5' UTR database suggests that 4% of human 5' UTRs harbor Alu sequences, indicating that the expression of many genes might be influenced by Alu repeats. These results illustrate the complex regulatory effects that retroelements can have on human gene expression.

Long terminal repeats are used as alternative promoters for the endothelin B receptor and apolipoprotein C-I genes in humans

To examine the potential regulatory involvement of retroelements in the human genome, we screened the transcribed sequences of GenBank and expressed sequence tag data bases with long terminal repeat (LTR) elements derived from different human endogenous retroviruses. These screenings detected human transcripts containing LTRs belonging to the human endogenous retrovirus-E family fused to the apolipoprotein CI (apoC-I) and the endothelin B receptor (EBR) genes. However, both genes are known to have non-LTR (native) promoters. Initial reverse transcription-polymerase chain reaction experiments confirmed and authenticated the presence of transcripts from both the native and LTR promoters. Using a 5'-rapid amplification of cDNA ends protocol, we showed that the alternative transcripts of apoC-I and EBR are initiated and promoted by the LTRs. The LTR-apoC-I fusion and native apoC-I transcripts are present in many of the tissues tested. As expected, we found apoC-I preferentially expressed in liver, where about 15% of the transcripts are derived from the LTR promoter. Transient transfections suggest that the expression is not dependent on the LTR itself, but the presence of the LTR increases activity of the apoC-I promoter from both humans and baboons. The native EBR-driven transcripts were also detected in many tissues, whereas the LTR-driven transcripts appear limited to placenta. In contrast to the LTR of apoC-I, the EBR LTR promotes a significant proportion of the total EBR transcripts, and transient transfection results indicate that the LTR acts as a strong promoter and enhancer in a placental cell line. This investigation reports two examples where LTR sequences contribute to increased transcription of human genes and illustrates the impact of mobile elements on gene and genome evolution.

Characterization of human MMTV-like (HML) elements similar to a sequence that was highly expressed in a human breast cancer: further definition of the HML-6 group

Previously, we found a retroviral sequence, HML-6.2BC1, to be expressed at high levels in a multifocal ductal breast cancer from a 41-year-old woman who also developed ovarian carcinoma. The sequence of a human genomic clone (HML-6.28) selected by high-stringency hybridization with HML-6.2BC1 is reported here. It was 99% identical to HML-6.2BC1 and gave the same restriction fragments as total DNA. HML-6.28 is a 4.7-kb provirus with a 5'LTR, truncated in RT. Data from two similar genomic clones and sequences found in GenBank are also reported. Overlaps between them gave a rather complete picture of the HML-6.2BC1-like human endogenous retroviral elements. Work with somatic cell hybrids and FISH localized HML-6.28 to chromosome 6, band p21, close to the MHC region. The causal role of HML-6.28 in breast cancer remains unclear. Nevertheless, the ca. 20 Myr old HML-6 sequences enabled the definition of common and unique features of type A, B, and D (ABD) retroviruses. In Gag, HML-6 has no intervening sequences between matrix and capsid proteins, unlike extant exogenous ABD viruses, possibly an ancestral feature. Alignment of the dUTPase showed it to be present in all ABD viruses, but gave a phylogenetic tree different from trees made from other ABD genes, indicating a distinct phylogeny of dUTPase. A conserved 24-mer sequence in the amino terminus of some ABD envelope genes suggested a conserved function.

Diversity of human endogenous retrovirus class II-like sequences

Class II human endogenous retroviruses (HERVs), often referred to as mouse mammary tumour virus (MMTV)-like or HERV-K elements, have similarities to several animal infectious retroviruses. Single clones from each of nine class II HERV groups (NMWV 1 to NMWV 9), isolated from a human breast cancer cell genomic library, were sequenced over a 244 bp stretch of the conserved reverse transcriptase region. These sequences were aligned to related exogenous and endogenous retroviruses and a phylogenetic tree was constructed. Sequences with more than 80% identity were considered as members of one group and we report here that the class II HERV family consists of at least ten groups. Three of the sequenced clones, from groups NMWV 3, 7 and 9, could not be related to any other previously identified elements and constituted their own groups. NMWV 8 had no similarity to any retroviral sequences in the sequenced region and is so far considered to be non-retroviral.

Human-specific integrations of the HERV-K endogenous retrovirus family

Several distinct families of endogenous retrovirus-like sequences (HERVs) exist in the genomes of humans and other primates. One of these families, the HERV-K group, contains members that encode functional proteins and that have been implicated in the etiology of insulin-dependent diabetes mellitus (IDDM). Because of potential functional and disease relevance, it is important to determine if there are HERV-K-associated genetic differences between individuals. In this study, we have investigated the divergence and evolutionary age of HERV-K long terminal repeats (LTRs). Thirty-seven LTRs, taken primarily from random human clones in GenBank, were aligned and grouped into nine clusters with decreasing sequence divergence. Cluster 1 sequences are 8.6% divergent, on average, whereas cluster 9 LTRs, represented by the LTRs of the fully sequenced HERV-K10 clone, show an average of only 1.1% divergence from each other. The evolutionary age of 18 LTRs from different clusters was then investigated by genomic PCR to determine presence or absence of the retroviral element in different primate species. LTRs from clusters of higher divergence were detected in monkeys and apes, whereas LTRs in clusters with lower divergence were acquired later in evolution. Notably, LTRs of cluster 9 were found only in humans at all nine loci examined. Genomic Southern analysis with an oligonucleotide probe specific for cluster 9 LTRs suggests that HERV-K elements with this type of LTR expanded independently in the genomes of humans and the great apes. This is the first report of endogenous retroviral integrations that are specific to humans and indicates that some HERVs have amplified much later than previously thought. These elements may still be actively transposing and may therefore represent a source of genetic variation linked to disease development.

Coamplification and dispersion of adjacent human endogenous retroviral HERV-H and HERV-E elements; presence of spliced hybrid transcripts in normal leukocytes

In an RT-PCR study of HERV-H spliced subgenomic transcripts, we found transcripts with HERV-H leader and protease-encoding sequences spliced to HERV-E integrase-encoding sequences in lymphocytes from healthy blood donors. In other cell types, including two T-cell leukemia cell lines, these transcripts were absent. The PCR fragments of the hybrid transcripts contained two open reading frames (ORFs). One was a hybrid HERV-H protease/HERV-E integrase ORF and the other was the HERV-E envelope surface glycoprotein ORF. Alternative splice products were also identified. The genomic DNA origin of the hybrid transcripts was shown to be a HERV-H element with a large 3'-end deletion, adjacent to a HERV-E element lacking the 5'-LTR. This hybrid structure was shown to be amplified and dispersed to six different human chromosomes. Thus, a relatively large part of full-length HERV-E elements (15-20%) is potentially under the transcriptional control of HERV-H LTRs. The HERV-H/HERV-E junction was present in multiple copies also in the chimpanzee and gorilla, but not in the orangutan or old world monkeys.

Structure and genomic organization of a novel human endogenous retrovirus family: HERV-K (HML-6)

Prototypic elements of a novel human endogenous retrovirus (HERV) family were identified and cloned from a human genomic library by the use of a pol fragment, HML-6, related to type A and type B retroviruses and class II HERVs. Out of 39 polhybridizing clones, five contained structures of full-length retroviral proviruses, with regions showing similarity to gag, pol and env, flanked by long terminal repeats (LTRs). Restriction mapping and partial sequence analysis of each full-length clone revealed few conserved restriction sites among HML-6 genomes, and about 20% sequence divergence over the reverse transcriptase region sequenced, suggesting that HML-6 constitutes a heterogeneous, but distinct family of elements belonging to the HERV-K superfamily. Sequence analysis of two clones, HML-6p and HML-6.17, revealed a lysine (K) tRNA UUU primer-binding site, and 40-68% nucleotide sequence similarity to LTR, gag, pro, pol and env regions of type B retroviruses and class II HERVs. HERV-K (HML-6) elements are present at about 30-40 copies per haploid genome. The HML-6 LTRs contain putative progesterone-responsive elements, which may be involved in the regulation of HML-6 expression. Furthermore, there are about 50 additional solitary HML-6 LTRs per haploid genome. Such LTRs were integrated within the pol region of two clones belonging to the same HML-6 family, indicating that some site preference may be involved in HERV integration.

Transcription of human endogenous retroviral sequences related to mouse mammary tumor virus in human breast and placenta: similar pattern in most malignant and nonmalignant breast tissues

The human genome contains a large variety of sequences related to the mouse mammary tumor virus (MMTV). We have investigated the range of expression of human endogenous retroviral sequences (HERVs) related to MMTV (human MMTV-like; HML) as RNA in 60 breast cancers, 8 nonmalignant breast tissues, and 9 placentas. This was monitored using HML group-specific oligonucleotide probes in hybridizations toward PCR amplificates of HML pol sequences and internal control. The degree of expression of five HML groups varied between individuals and between tissues. On average, all HML groups were less expressed in breast tissues than in placenta. The hybridization signals of some HML RNAs were strongly correlated, indicating a nonstochastic mechanism and a concerted regulation of their expression. The PCR product from one breast cancer (BC 6), which gave an exceptionally high expression with probe hml-6, with a 20 times stronger signal than the rest of the cancers, was cloned and sequenced. The HML-6 transcript sequences were homogeneous in BC 6. The most predominant clone derived from the cancer was used as a probe in Southern hybridizations. The same restriction fragments were detected in human breast tissues, PBMCs (peripheral blood mononuclear cells), and breast cancer cell lines, except for one of the breast cancers and one of the nonmalignant breast tissues, which gave different banding patterns. A comparison of HML expression in normal and malignant breast tissue from the same individual would have been more precise than our comparison of samples from different persons. Bearing this limitation in mind, with a single exception, human MMTV-like sequences were not more actively expressed in malignant than in nonmalignant breast tissues. Nevertheless, an interesting diversity in their expression, especially between individuals, was found.

Differential expression of human endogenous retroviral sequences similar to mouse mammary tumor virus in normal peripheral blood mononuclear cells

Mouse mammary tumor virus (MMTV) is a retrovirus that causes breast cancer in certain strains of mice. In a previous study we identified, by sequencing clones from human lymphocytes, six groups with similarities to MMTV. Using a primer pair derived from pol sequences conserved within types A, B, and D retroviruses and probes from the six human MMTV-like (HML-1 to HML-6) groups in an internally controlled hybridization assay we investigated the normal variation of expression in PBMCs. Variations occurred within all groups but was most significant within group HML-1, where hybridization signals differed by more than 500-fold between individuals. Groups HML-2 and HML-3 showed consistently stronger hybridization signals than groups HML-1 and HML-5, while group HML-6 resulted in weak signals for all individuals. Stringent hybridization of the amplified cDNA to 20 individual HML clones also demonstrated a marked heterogeneity of expression. Hybridization signals from some groups and sequences were found to be correlated, either in a positive or negative fashion. RNA isolated from PBMCs collected from two donors at four different time points (in the morning and in the afternoon on the same day, repeated 1 week later) was also analyzed using the six hml probes. A small variation in hybridization signals was seen in samples collected on the same day, but a larger difference was observed in samples taken 1 week later. The correlations and the differences in the expression of HMLs between individuals implicate a complex transcriptional regulation system of these sequences.

Characterization of novel reverse transcriptase encoding human endogenous retroviral sequences similar to type A and type B retroviruses: differential transcription in normal human tissues

The polymerase chain reaction was used to amplify genomic DNA and reverse-transcribed RNA from human lymphocytes, using primers derived from conserved regions within the retroviral reverse transcriptase. Sequencing of 33 cloned amplification products revealed that a variety of sequences with similarity to mouse mammary tumor virus, mouse intracisternal A particle, and human endogenous retrovirus K10 were detected with this primer pair. The sequences were divided into six subgroups, with a nucleotide sequence dissimilarity of about 25% between the subgroups. Members within five of the subgroups were most closely related to human endogenous retrovirus K10 and mouse mammary tumor virus, whereas sequences of the sixth subgroup also showed similarity to mouse intracisternal A particle. Ten of the sequences had open reading frames with preference for silent mutations at conserved sites. Southern blot analysis showed that some HML (human endogenous MMTV-like) subgroups (HML-4 and HML-5) were present in a few copies (about 5), whereas others (HML-1 to HML-3 and HML-6) were present in at least 10 to 20 copies per genome. Northern (RNA) blot analysis revealed that several of the subgroups are differentially expressed in human normal tissues. A complex pattern of transcripts from about 12 to 1.4 kb was found in several of the tissues tested. However, the most abundant expression was detected in lung (all subgroups), skeletal muscle (HML-4 and HML-5), placenta (HML-2 and HML-5), and kidney (HML-2, HML-3 and HML-5). Expression of reverse transcriptase sequences in human tissues may have biological consequences. The described sequences are similar to elements which cause carcinoma and are immunoregulatory in mice. It remains to be seen whether human sequences also have such functions.

Sequence variation of human endogenous retrovirus ERV9-related elements in an env region corresponding to an immunosuppressive peptide: transcription in normal and neoplastic cells

Evolutionarily conserved sequences corresponding to an immunosuppressive region in retroviral transmembrane proteins were amplified by the polymerase chain reaction from human genomic DNA and reverse-transcribed RNA from one glioma, three pieces of macroscopically normal brain tissue, kidney, lymphocytes, cultured embryonic lung cells, and a rhabdomyosarcoma cell line. Amplification products (125 bp) from DNA and RNA from the glioma and RNA from one normal piece of brain tissue were cloned and sequenced (45 clones). A variety of sequences similar to ERV9 (75 to 93%) were identified. Amplification products were immobilized on nylon filters and hybridized to four different synthetic oligonucleotides derived from the sequenced clones. Sequences without the stop codon seen in ERV9 in this region, possibly encoding functional immunosuppressive proteins, were present in RNA amplificates from all samples. The various cell types showed different hybridization patterns with the four probes. The open reading frame sequences were identified in genomic Southern blots, one probe detecting about 10 copies and another detecting a single copy. Northern (RNA) blots of mRNA from various normal human tissues revealed 2.5-kb (e.g., lung) and 10-kb (e.g., placenta) transcripts hybridizing to one of the probes.

Expression of human endogenous retroviral sequences in peripheral blood mononuclear cells of healthy individuals

The polymerase chain reaction was used to detect expression of retroviral sequences with oligonucleotide primers derived from conserved regions of the retroviral genome. Four primer pairs derived from gag and one from pol were used in amplification of reverse-transcribed total RNA prepared from peripheral blood mononuclear cells of seven blood donors. The amplification pattern was the same from each of the seven samples. Sequencing of cloned amplification products revealed that at least three subclasses of sequences related to the human endogenous retroviruses (HERV) RTVL-H, HERV-E and HERV-K, are expressed in peripheral blood mononuclear cells of healthy individuals. This has not been previously reported.

Identification of regions of HIV-1 p24 reactive with sera which give "indeterminate" results in electrophoretic immunoblots with the help of long synthetic peptides

We analyzed nine sera from persons unlikely to be HIV infected which had an IgG reactivity directed against HIV-1 p24, and in two cases also to its precursor p55, but to no other HIV proteins, nor to proteins of the H9 host cell, in electrophoretic immunoblots (EIB). These sera are also referred to as having an indeterminate HIV EIB pattern or as HIV antibody false positive sera. Seven of nine sera reacted with longer (61-77 amino acids) and none with shorter (17-25 amino acids) p24-derived peptides in enzyme immunoassays (EIAs). This is compatible with a conformational (discontinuous) nature of the epitopes involved in many false positive HIV-1 p24 antibody reactions. Four sera reacted with an N-terminal, one with an internal, and two with a C-terminal fragment. Each of the seven sera thus only reacted with one of the long p24 peptides. The specificity and singularity of the reaction was further demonstrated by competition and/or absorption experiments with synthetic peptides. In contrast, 18 of 20 confirmed HIV-1+ sera with p24 reactivity in EIB reacted with at least one and often several of the longer peptides, most frequently the C-terminal one. Thus, the distribution of peptide reactivity of true HIV-1 antibody-positive sera was different from that of the falsely reactive sera. According to two of several explanations, these antibodies may have arisen because of (1) molecular mimicry by chance or by functional selection, (2) immunization by activation, noninfectious exposure, or infection involving non-HIV endogenous or exogenous retroviral antigens. The latter gains some support from our finding of antibody reactions with capsid proteins of the simian viruses, simian sarcoma-associated virus (SSAV), and Mason-Pfizer monkey retrovirus in some of the p24 +/- p55 reactive sera.