HIV-associated malignant lymphomas in Kenya (Equatorial Africa)

The clinical and pathological features of acquired immune deficiency syndrome (AIDS)-related lymphomas, including their relationship with other viruses, such as Epstein-Barr virus (EBV) and human herpes virus-8 (HHV8), have been the subject of several studies from North America and Europe. No consistent data have been reported in Africa, where AIDS runs an epidemiological and clinical course different from that observed in Western countries. We retrospectively evaluated the presence of human immunodeficiency virus (HIV), HHV8, and EBV in 146 cases of malignant lymphomas collected in Kenya (Equatorial Africa), with the use of polymerase chain reaction (PCR) and in situ hybridization (ISH). The PCR technique confirmed HIV infection in 16 HIV-seropositive subjects (11%) and showed the presence of HIV sequences in five additional cases (3%) in which the occurrence of lymphoma was the only clinical manifestation. Our findings suggest that AIDS-related lymphomas are not pathogenetically homogenous, and different mechanisms may contribute to lymphomagenesis in these severely immunocompromised patients. In our series, no association of Hodgkin's disease (HD) with HIV infection could be shown. Among non-HIV-related lymphomas, EBV was present in 94% of Burkitt lymphoma (BL) occurring in patients younger than 15 years of age, in 87% of HD independently of age, sex, and histological types, in 60% of anaplastic large cell lymphoma (ALCL), and to a lesser extent (13%) in large B-cell lymphoma (LBCL) cases. Only one tumor, a case of HD, showed HHV8 by PCR.

Long-read direct infrared sequencing of crude PCR products for prediction of resistance to HIV-1 reverse transcriptase and protease inhibitors

Patients infected with human immunodeficiency virus type 1 (HIV-1) are being treated with a number of different combinations of antiretroviral compounds that target the essential viral enzymes reverse transcriptase and protease. Different sets of HIV-1 mutations that confer drug resistance have been well defined; they allow reasonable prediction of the drug sensitivity pattern from analysis of the HIV-1 genotype in vivo. Since periodical monitoring of genotypic resistance is expected to improve clinical management in a large number of infected patients, practical and cost-effective methods are highly desirable to set at least medium-scale sequencing in clinical diagnostic settings. We present a complete protocol for direct sequencing of HIV-1 reverse transcriptase and protease-coding regions. Features making the system amenable to routine clinical use include: 1. Highly robust presequencing steps (plasma RNA extraction, reverse transcription, and nested PCR); 2. Direct use of the crude unpurified PCR product as the sequencing template; and 3. Use of infrared-labeled sequencing primers consistently allowing long reads, thus obviating the need for sequencing of both DNA strands.

Fatal herpesvirus 6 encephalitis after unrelated bone marrow transplant

A complex pattern of neurological dysfunctions with generalized seizures and visual allucinations, but without focal signs, suddenly arose 20 days after an unrelated bone marrow transplant for chronic myelogenous leukemia (CML) in a 13-year-old girl, accompanied by signs of acute skin graft-versus-host disease (GVHD). Magnetic resonance imaging (MRI) revealed multiple bilateral foci of signal abnormalities, which were exclusively localized in the grey matter, sparing the white. Extensive microbiological and virological assays of cerebrospinal fluid (CSF) allowed the identification of HHV-6, variant A, DNA. Further progression of both neurological alterations and of skin and gut GVHD led to a fatal outcome 2 weeks later. A retrospective analysis of both the recipient and donor mononuclear cell suspensions supported the hypothesis that HHV-6 had been acquired from the donor with the bone marrow graft. This report suggests a pathogenetic role of HHV-6 in viral encephalitis in immunocompromised bone marrow transplant (BMT) recipients, and its possible association with GVHD.

Evaluation of the presence of 2-LTR HIV-1 unintegrated DNA as a simple molecular predictor of disease progression

In a preliminary cross-sectional analysis of 109 human immunodeficiency virus type 1 (HIV-1)-infected subjects the presence of 2-long terminal repeat (LTR) unintegrated circular HIV-1 DNA in peripheral blood mononuclear cells (PBMC) was found to be associated with both symptomatic infection (P = 0.0037) and low CD4 counts (P = 0.0004). To investigate the prognostic significance of the presence of 2-LTR HIV-1 DNA, a subset of 23 2-LTR-negative and 25 2-LTR-positive asymptomatic individuals were followed up for 12-24 months. The two groups did not differ in terms of baseline CD4 counts, zidovudine (ZDV) therapy, and duration of HIV-1 infection. Longitudinal analysis of CD4 values did not indicate a significantly different CD4 outcome between the two groups. However, when only ZDV-treated subjects were considered, a significant (P = 0.042) decrease in CD4 counts was found at month 24 with respect to baseline in 2-LTR-positive (n = 12) but not in 2-LTR-negative (n = 11) patients. Moreover, when > 40% CD4 loss from baseline and/or development of CDC stage B or C symptoms were considered as indicators of disease progression, there was a significantly higher number of events in the whole 2-LTR-positive group than in the whole 2-LTR-negative group (P = 0.0197 at month 12, P = 0.0299 at month 18, P = 0.0373 at month 24). Thus, the presence of 2-LTR HIV-1 DNA in PBMC merits further investigation as a simple, qualitative, molecular predictor of disease progression and decreased response to antiretroviral therapy.

Focal myositis: a polymerase chain reaction analysis for a viral etiology

Focal myositis (FM) is a benign inflammatory condition that may clinically simulate a soft tissue sarcoma. It was first described in 1977, and only approximately 30 cases have been reported to date, yet this entity is probably more frequent. The pathogenesis of FM is totally unknown. It has been proposed that it represents a nodular form of myositis, which can evolve into polymyositis, but this hypothesis has not been confirmed by follow-up studies. We describe seven cases of FM, five of which have never been reported before. Histology of the lesions was very similar, showing a destructive inflammatory myopathy with evidence of regeneration. Our study attempted to better understand the pathogenesis of this focal inflammatory myopathy. We performed a polymerase chain reaction study to explore the presence of a number of viral infectious agents in the inflammed tissue. The present study failed to show the presence of a known viral agent with a recognized tropism for myofibers. With a panel of lymphoid cell markers, we also characterized the phenotype of the inflammatory infiltrate that was composed of many T-lymphocytes with few CD4+ cells. Lastly, we reviewed the published cases and discuss the possible pathogenesis.

Zidovudine resistance mutations and human immunodeficiency virus type 1 DNA burden: longitudinal evaluation of six patients under treatment

Zidovudine (ZDV) is by far the most widely used drug to counteract human immunodeficiency virus type 1 (HIV-1) infection, both in monotherapy and in combination therapy regimens. However, the majority of patients under prolonged ZDV therapy have been shown to harbour HIV-1 mutant genomes displaying reduced sensitivity to the drug in vitro. In order to investigate the pathogenic role of in vitro resistance to ZDV, six HIV-1-infected ZDV-treated subjects were evaluated longitudinally (mean follow-up 28.5 months, range 12-39 months) for HIV-1 DNA load in peripheral blood mononuclear cells (PBMC) and for the presence of HIV-1 pol gene mutations responsible for ZDV resistance. Quantitation of HIV-1 DNA was performed by competitive polymerase chain reaction (cPCR) and the pol genotype was determined by direct sequencing of PCR products. All of the six patients developed one or more of the HIV-1 pol mutations known to confer resistance to ZDV in vitro (Met41-->Leu, Asp67-->Asn, Lys70-->Arg, Thr215-->Phe/Tyr, Lys219-->Gln/Glu). A temporal association was found between HIV-1 DNA burden and the level of ZDV resistance, as predicted on the basis of the pol genotype (genotypic resistance). Both virus load and ZDV resistance were inversely correlated with CD4+ cell counts. These results are compatible with a direct in vivo pathogenetic role for pol gene mutations shown to be involved in resistance to ZDV in vitro. Monitoring the degree of genotypic resistance to ZDV and to other antiretroviral drugs should be considered in designing protocols for the management of treated patients.

Neuronal intranuclear inclusion disease: polymerase chain reaction and ultrastructural study of rectal biopsy specimen in a new case

We report the case of a boy with neuronal intranuclear inclusion disease in whom the diagnosis was made by examination of a rectal biopsy specimen. Intranuclear inclusions were observed in the Auerbach and Meissner plexuses. In an attempt to understand the physiopathology of this very rare disease, we performed polymerase chain reaction (PCR) and reverse transcriptase-PCR analysis for viral nucleic acids of human immunodeficiency virus type 1 (HIV-1), HIV-2, human cytomegalovirus and measles virus. No viral nucleic acids were detected in the biopsy specimen.

Concordance between polymerase chain reaction and antibody detection in the diagnosis of human immunodeficiency virus type 1 infection

A highly sensitive nested polymerase chain reaction (PCR) protocol was used to detect human immunodeficiency virus type 1 (HIV-1) DNA in peripheral blood mononuclear cells from 271 HIV-1-seropositive patients, 240 HIV-1-seronegative subjects at increased risk for HIV-1 infection, 51 serologically indeterminate individuals, and 120 healthy blood donors. PCR was carried out in a multiplex nested configuration with pol and env region primer sets. HIV-1 DNA was detected in all of the HIV-1 seropositive patients. In contrast, HIV-1 DNA was not detected in any of the either seronegative or serologically indeterminate subjects. Only one of 37 seronegative regular sexual partners of HIV-1-infected patients who were followed longitudinally was found to seroconvert to HIV-1. However, HIV-1 DNA and antibody results were concordant in the four samples obtained from this subject prior to and after seroconversion. These results show an excellent concordance between HIV-1 DNA and antibody detection for diagnosis of HIV-1 infection and suggest that long-term HIV-1 infection in the absence of detectable antibody is likely to occur at a very low frequency.

Identification of Mycobacterium tuberculosis complex, Mycobacterium avium and Mycobacterium intracellulare by selective nested polymerase chain reaction

A nested polymerase chain reaction (PCR) procedure was devised for identification of mycobacteria. The outer reaction exploiting genus-specific sequences on the 16S rRNA gene was able to amplify specifically strains of the genus Mycobacterium. The identification of Mycobacterium tuberculosis complex, Mycobacterium avium and Mycobacterium intracellulare was accomplished by selective reamplification of the outer PCR product in three distinct inner amplifications exploiting species-specific primers mapping to a hypervariable region of mycobacterial 16S rRNA. Detection of mycobacteria, other than those for which species-specific primers were used, was accomplished by adding a supplementary genus-specific upper primer to one of the inner reactions. Specificity of amplification was confirmed for clinical isolates and reference strains of different mycobacterial species with the exception of a M. intracellulare type 7 strain which was recognized as M. avium. The amplification protocol presented thus provides a reliable and cost-effective way for identification of clinically relevant mycobacteria.

Dosage of Tn916 circular intermediates in Enterococcus faecalis

Upon excision, conjugative transposon Tn916 forms a nonreplicating circular intermediate (CI), which is essential both for transposition and conjugal transfer. In this work we developed an assay to quantify the circular forms of Tn916. By this method we defined a new measurable trait of Tn916-carrying strains: the "CI copy number." CI dosage was performed by nested PCR (with primers designed on Tn916 termini) in a limiting dilution assay, where Poisson statistics were used to calculate the number of PCR amplification targets from the proportion of the negative endpoints. The number of CI was normalized to the number of bacterial chromosomes. This method enabled us to study the relationship between CI copy number, presence of tetracycline (the resistance marker of Tn916) in the culture medium, and conjugation frequency. Three isogenic strains of Enterococcus faecalis OG1 with Tn916 inserted at different sites on the chromosome were investigated for CI content. CI copy number varied depending on the strain, ranging between 7.8 and 610 copies per 10(6) chromosomes. Growth in liquid media containing tetracycline provoked an important increase both in CI copy number and conjugation frequency. This effect was more marked in low-frequency donors. While cell-cell contact during filter mating did not produce an increase in CI copy number, Tn916 conjugation frequency was found to be dependent on CI copy number in donor cells. The dose-response curve showed a linear relationship with a slope of 0.74, for the entire range of conjugation frequencies tested (from 5.1 x 10(-8) to 2.8 x 10(-6) transconjugants per donor.

Increased reliability of selective PCR by using additionally mutated primers and a commercial Taq DNA polymerase enhancer

A reliable selective PCR procedure that combines the use of additionally mutated primers with the specificity-enhancing properties of a commercial preparation (Perfect Match, Stratagene) is described. The human immunodeficiency virus type 1 pol gene point mutations known to confer in vitro resistance to azidothymidine were examined as a model for optimization of the assay. The usual strategy of deliberately introducing an additional mismatch 1 residue from the 3' end in the wild-type and mutant primers did not allow reproducible discrimination between wild-type and mutant target sequences. Addition of minimal amounts of Perfect Match to the same PCR mixtures resulted in a significantly enlarged range of selective annealing temperatures, providing a valuable and cost-effective means for reliable detection of known mutations by selective PCR.

Low human immunodeficiency virus type 1 (HIV-1) DNA burden as a major cause for failure to detect HIV-1 DNA in clinical specimens by PCR

To determine the sensitivity of a nested PCR procedure for detecting human immunodeficiency virus type 1 DNA in clinical specimens, 553 peripheral blood mononuclear cell samples obtained from 268 human immunodeficiency virus type 1-seropositive subjects were assayed by use of two independent primer sets for each sample. Overall, 1,088 of 1,106 (98.37%) reactions were positive. Investigation of the negative reactions showed that a low viral burden in some infected subjects, rather than primer-template mismatches, was the primary cause for the false-negative PCR results.

Optimal conditions for detection of human immunodeficiency virus type 1 DNA by polymerase chain reaction with nested primers

An assessment of optimal conditions for nested primer amplification of low copy number target DNA sequences was made using a human immunodeficiency virus type 1 (HIV-1) model. In this polymerase chain reaction (PCR) strategy, an outer primer pair is first used to amplify the target sequence and a fraction of the amplification product is further amplified with a pair of inner (nested) primers. Several methodological parameters were evaluated, including number of cycles in the first and second step of the reaction, proportion of preamplified material to be used as the template for the second amplification, concentrations of primers, deoxynucleotides, and Taq DNA polymerase in the outer and inner PCR. The two-step PCR required minimal amounts of reaction components and was shown to be highly flexible, resulting in exquisite and specificity over a wide range of technical conditions. Potential drawbacks of this practical and effective amplification procedure are also discussed.

Simultaneous amplification of multiple HIV-1 DNA sequences from clinical specimens by using nested-primer polymerase chain reaction

A sensitive and specific polymerase chain reaction (PCR) protocol with nested primers was developed for simultaneous amplification of three independent human immunodeficiency virus type 1 (HIV-1) DNA sequences from clinical specimens. DNA samples were first amplified with gag, pol, and env outer primer pairs and then with the corresponding three inner primer pairs in the same two-step reaction. Detection of the different amplification products was readily accomplished by simple agarose gel electrophoresis of the reaction product, even when starting with a single copy of HIV-1 DNA. Equivalent amounts of the three PCR products were generated, provided that the relative concentrations of the inner primer pairs were optimized. In addition, a beta-globin control primer pair could be conveniently included in the internal amplification step to verify that the DNA sample was suitable for PCR analysis. One nested multiplex PCR test was sufficient to detect HIV-1 DNA in all of 80 HIV-1-seropositive individuals and none of 50 HIV-1-seronegative healthy blood donors. The nested multiplex PCR procedure provides an attractive means for simple, rapid, and cost-effective direct detection of HIV-1 DNA in patient samples.

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.

Sarcoidosis and infections by human lymphotropic viruses

In sera of 38 patients with sarcoidosis, assayed for antiviral antibody to Rubella, Measles, Cytomegalovirus (CMV), adenovirus, Epstein-Barr virus (EBV), human immunodeficiency virus (HIV), different incidence of seropositivity have been found, according to the virus assayed. Interestingly all patients were seropositive to rubella virus with high titres compared to data obtained from normal age matched population. These data indicate that in Sarcoidosis an altered antibody response of post-primary type can be found.

NMR investigation of cell cultures: early detection of infection by Herpes simplex virus type 2 and transformation

The water proton Nuclear Magnetic Resonance (NMR) spin-lattice relaxation rates were measured in suspension of uninfected and Herpes simplex virus type 2-infected WI-38 diploid cells and shown to allow reliable detection of (i) the early signs of productive infection, and (ii) the tendency to undergo either spontaneous or virus-induced transformation. In addition, NMR investigation of several transformed cell lines currently and previously established from WI-38 cells clearly indicated that the NMR relaxation parameter is a suitable tool for assessment of the level of malignancy, as revealed by in vivo oncogenicity tests in immunosuppressed mice.

Live-cell immunofluorescence for detection of human immunodeficiency virus type 1 (HIV-1)-related antigens in peripheral blood mononuclear cells from HIV-1 seropositive individuals

Live-cell indirect immunofluorescence was used to detect HIV-associated antigens in fresh uncultured peripheral blood mononuclear cells from 29 HIV-seropositive subjects. Conventional fixed-cell immunofluorescence and live-cell immunofluorescence were run in parallel on each sample using monoclonal antibodies directed against HIV gag and env gene products. Sera from the same patients were also tested for HIV antigen by a sandwich enzyme immunoassay. Results strongly indicate that nondenaturing live-cell immunofluorescence is much more sensitive for detection of HIV-associated antigens and may be useful in the diagnosis of HIV infection as well as in the study of pathogenesis.