Biological variation and quality control of plasma human immunodeficiency virus type 1 RNA quantitation by reverse transcriptase polymerase chain reaction

Enhancing the health of women living with HIV: the SMART/EST Women's Project

THE PRINCIPAL OBJECTIVE OF THESE MULTISITE STUDIES (FLORIDA, NEW YORK, NEW JERSEY: epicenters for human immunodeficiency virus [HIV] among women) was to develop and implement effective combinations of behavioral interventions to optimize the health status of the most neglected and understudied population affected by the acquired immunodeficiency syndrome (AIDS) epidemic in the United States: poor women of color living with HIV. The two studies enrolled nearly 900 women randomly assigned to "high intensity" (cognitive-behavioral stress management training combined with expressive-supportive therapy [CBSM]+ group) or "low intensity" (individual psychoeducational program) treatment conditions over a period of 9 years. The initial study of the stress management and relaxation training/expressive-supportive therapy (SMART/EST) Women's Project (SWP I) focused on reducing depression and anxiety, as well as improving self-efficacy and overall quality of life for women with case-defined AIDS. Findings from this study demonstrated the utility of CBSM+ in reducing distress (depression, anxiety) and denial, while improving social support, self-efficacy, coping skills, and quality of life. The second study (SWP II), which included all women living with HIV, extended these findings by demonstrating that exposure to CBSM+ significantly improved the ability of the participants to take advantage of a health behavior change program encouraging the adoption and maintenance of healthier lifestyle behaviors (high levels of medication adherence, appropriate nutritional intake and physical activity, safer sexual practices, and reduced alcohol use/abuse) essential for optimal health in the context of living with HIV. SWP II also determined that the intervention program was equally beneficial to less-acculturated segments of the affected population (ie, non-English speaking HIV+ women) through the creation of culturally and linguistically sensitive Spanish and Creole versions of the program. A third study (SWP III) is currently underway to "translate" this evidence-based treatment program into Community Health Centers in Miami, New York City, and metropolitan New Jersey.

Collection and preservation of frozen microorganisms

The storage of the different microorganisms over long periods is necessary to ensure reproducible results and continuity in research and in biomedical processes and also for commercial purposes. Effective storage means that a microorganism is maintained in a viable state free of contamination or genetic drift and must be easily restored without genotypic or phenotypic alterations to its original characteristics and properties. To this end, different techniques have been described and advances in cryopreservation technology have led to methods that allow low-temperature maintenance of a variety of cell types, minimizing the risks of genetic change and are now recommended for long-term storage of most microorganisms.This chapter summarizes the most important steps and components in the process of low- and -ultra-low temperatures freezing of bacteria, parasites, yeasts and fungi, viruses, and recombinant microorganisms.

Clinical prognostic value of RNA viral load and CD4 cell counts during untreated HIV-1 infection--a quantitative review

Background

The prognostic value of CD4 counts and RNA viral load for identifying treatment need in HIV-infected individuals depends on (a) variation within and among individuals, and (b) relative risks of clinical progression per unit CD4 or RNA difference.

Methodology/Principal Findings

We reviewed these measurements across (a) 30 studies, and (b) 16 cohorts of untreated seropositive adults. Median within-population interquartile ranges were 74,000 copies/mL for RNA with no significant change during the course of infection; and 330 cells/µL for CD4, with a slight proportional increase over infection. Applying measurement and physiological fluctuations observed on chronically infected patients, we estimate that 45% of population-level variation in RNA, and 25% of variation in CD4, were due to within-patient fluctuations. Comparing a patient with RNA at upper 75^th centile with a patient at median RNA, 5-year relative risks were 1.4 (95% CI 1.2–1.7) for AIDS and 1.5 (1.3–1.9) for death, without change over the course of infection. In contrast, for a patient with CD4 count at the lower 75^th centile, relative risks increased from 1.0 at seroconversion to maxima of 6.3 (4.4–8.9) for AIDS and 5.5 (2.7–10.1) for death by year 6, when the population median had fallen to 300 cells/µL. Below 300 cells/µL, prognostic power did not increase, due to a narrower CD4 range.

Conclusions

Findings support the current WHO recommendation (used with clinical criteria) to start antiretroviral treatment in low-income settings at CD4 thresholds of 200–350 cells/µL, without pre-treatment RNA monitoring – while not precluding earlier treatment based on clinical, socio-demographic or public health criteria.

The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments

BACKGROUND

Currently, a lack of consensus exists on how best to perform and interpret quantitative real-time PCR (qPCR) experiments. The problem is exacerbated by a lack of sufficient experimental detail in many publications, which impedes a reader's ability to evaluate critically the quality of the results presented or to repeat the experiments.

CONTENT

The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines target the reliability of results to help ensure the integrity of the scientific literature, promote consistency between laboratories, and increase experimental transparency. MIQE is a set of guidelines that describe the minimum information necessary for evaluating qPCR experiments. Included is a checklist to accompany the initial submission of a manuscript to the publisher. By providing all relevant experimental conditions and assay characteristics, reviewers can assess the validity of the protocols used. Full disclosure of all reagents, sequences, and analysis methods is necessary to enable other investigators to reproduce results. MIQE details should be published either in abbreviated form or as an online supplement.

SUMMARY

Following these guidelines will encourage better experimental practice, allowing more reliable and unequivocal interpretation of qPCR results.

Bio-banking in microbiology: from sample collection to epidemiology, diagnosis and research

Millions of biological samples, including cells of human, animal or bacterial origin, viruses, serum/plasma or DNA/RNA, are stored every year throughout the world for diagnostics and research. The purpose of this review is to summarize the resources necessary to set up a bio-banking facility, the challenges and pitfalls of sample collection, and the most important techniques for separation and storage of samples. Biological samples can be stored for up to 30 years, but specific protocols are required to reduce the damage induced by preservation techniques. Software dedicated to biological banks facilitate sample registration and identification, the cataloguing of sample properties (type of sample/specimen, associated diseases and/or therapeutic protocols, environmental information, etc.), sample tracking, quality assurance and specimen availability. Bio-bank facilities must adopt good laboratory practices and a stringent quality control system and, when required, comply with ethical issues.

Evaluation of the Cobas AmpliPrep/Cobas Amplicor HIV-1 Monitor Ultrasensitive Test: comparison with the Cobas Amplicor HIV-1 Monitor test (manual specimen preparation)

In this preliminary study, we evaluated the performance of the Cobas AmpliPrep/Cobas Amplicor HIV-1 Monitor Ultrasensitive Test (CAP; Roche Molecular Systems, Branchburg, NJ) for automated specimen preparation and quantitative detection of human immunodeficiency virus type 1 (HIV-1) RNA and compared it to the Cobas Amplicor HIV-1 Monitor Ultrasensitive Test (MCA; Roche), which includes a manual sample preparation protocol. A dilution panel of a patient sample was prepared. Additionally, 584 EDTA plasma samples were collected from HIV-1 infected patients. Reproducibility was estimated with six assay runs using the dilution panel. The inter-assay coefficient of variation ranged from 39.4 to 48.4% (CAP assay) and from 34.3 to 45.6% (MCA assay), whereas the intra-assay coefficient of variation ranged from 6.2 to 58.0% (CAP assay) and from 4.4 to 57.3% (MCA assay). Comparison of CAP assay results with the HIV-1 copy number of the dilution panel determined by the MCA assay resulted in a good agreement, although the CAP results were found to be slightly lower. A significant correlation between both test systems was found when clinical samples were analyzed. The mean viral load of 152 samples, which were within the linear range of both tests, was 3.70 log(10) HIV-1 copies/ml by the CAP assay compared to 3.73 by the MCA assay. In conclusion, we could demonstrate that the new Cobas AmpliPrep/Cobas Amplicor HIV Monitor Ultrasensitive Test is reproducible and sensitive. In comparison to the assay with manual extraction, no significant difference in HIV-1 RNA copy numbers was observed.

Stability of plasma human immunodeficiency virus load in VACUTAINER PPT plasma preparation tubes during overnight shipment

VACUTAINER PPT plasma preparation tubes were evaluated to determine the effects of various handling and shipping conditions on plasma human immunodeficiency virus (HIV) load determinations. Plasmas obtained from PPT tubes stored and shipped under nine different conditions were compared to conventional EDTA tube plasmas stored at -70 degrees C within 2 h after phlebotomy. Compared to viral loads in frozen EDTA plasma, those in PPT tube plasma that was frozen immediately and either separated or shipped in situ were not significantly different. Viral loads in PPT tube plasma after storage for 6 h at either room temperature or 4 degrees C, followed by shipment at ambient temperature or on wet or dry ice, were not significantly different from baseline viral loads in EDTA or PPT plasma. The results of this study indicate that the HIV load in PPT tube plasma is equivalent to that in standard EDTA plasma. Plasma viral load is not affected by storage or shipment temperature when plasma is collected in PPT tubes. Furthermore, plasmas can be shipped in spun PPT tubes, and the tubes provide a safer and more convenient method for sample collection and transport than regular EDTA tubes.

Relationship of incremental specimen volumes and enhanced detection of human immunodeficiency virus type 1 RNA with nucleic acid amplification technology

The relationship between specimen input volume and the frequency of reported human immunodeficiency virus type 1 (HIV-1) RNA copy numbers by nucleic acid amplification technology (the NASBA HIV-1 RNA QT system) was investigated. Results obtained with both clinical specimens and dilution panels indicated that both the absolute number of reported results and the reported HIV-1 RNA copy number were directly proportional to the specimen input volumes evaluated (0.1, 0.5, and 1.0 ml). Conversion of the reported HIV-1 RNA copy numbers to a constant 1.0-ml volume indicated that the numerical relationship among the specimen input volumes and the HIV-1 RNA copy numbers was multiplicative. The HIV-1 RNA copy numbers reported for the 0.5-ml input volume were approximately 5-fold increased over those reported for the 0.1-ml input volume, and those reported for the 1.0-ml input volume were 10-fold increased over those reported for the 0.1-ml input volume. For the specimen input volumes investigated, a common linear range of 264 to 5,400,000 HIV-1 RNA copies was observed. The use of increased specimen input volumes did not result in a loss of assay specificity, as the results reported for specimens from 50 seronegative blood donors were negative at all three specimen input volumes. In conclusion, an increase in the input volume of specimens analyzed by nucleic acid amplification technology can be useful for the enhanced detection of HIV-1 RNA.

A sensitive, non-radioactive quantitative method for measuring IL-4 and IL-4delta2 mRNA in unstimulated cells from multiple clinical samples, using nested RT-PCR

Measurements of IL-4 mRNA directly from clinical samples are technically difficult as IL-4 is a low copy number cytokine. Moreover, most existing studies involving RT-PCR are confused by the use of primers which simultaneously amplify cDNA of IL-4 and its splice-variant (IL-4delta2). We describe a sensitive nested RT-PCR method to quantify mRNA expression of IL-4 and IL-4delta2 separately. It involves a simple method of generating cRNA standards without cloning. The use of external synthetic RNA standards, for which we validate that amplification kinetics are equivalent to the target, obviates the need for multiple sample dilutions. The assay is sensitive enough to measure IL-4 and IL-4delta2 mRNA expression in unstimulated PBMCs of normal subjects, and the reproducibility and throughput make this assay suitable for use in clinical studies with multiple samples.

Immobilized sample amplification for quantitative determination of retroviruses

Immobilized sample amplification (ISA) is a novel method for amplification, detection, monitoring, and quantitative determination of nucleic acids from a minute amount of sample. We present here a novel quantitative ISA assay for retroviruses using a replication-defective recombinant retrovirus as a model retrovirus. Samples, as small as 5 to 10 microl or as large as 1 ml or more in volume, are readily immobilized on a nylon or polyester matrix. Retroviral RNA is directly amplified following the rehydration of the immobilized samples, thus eliminating the needs for retroviral RNA extraction. An ISA assay of a 10-microl viral sample generates results equal to or better than that of RT-PCR on equivalent amount RNA isolated from larger sample volumes. Recovery of RNA from small volumes, such as 10 microl, is almost impossible, whereas ISA assay detects retroviruses from as small as 1 to 5 microl of viral samples containing 10(4) cfu/ml determined by colony-forming assay. Extraction of RNA from a small amount of infectious viral samples not only is a difficult, biohazardous procedure, but also introduces random errors which contribute to variability in viral quantitation. Since the ISA method eliminates the isolation/extraction of the nucleic acids, it significantly shortens the handling time for the biohazardous materials and simplifies the procedure for analyzing small quantities of biological samples. This method detects less than 10 infectious retroviral particles as determined by both colony-forming assay and electron microscope studies. The format and protocol of this quantitative ISA assay can be easily automated to fit into numerous platforms, thus making it attractive for laboratory automation.

Clinical cross-resistance between the HIV-1 protease inhibitors saquinavir and indinavir and correlations with genotypic mutations

OBJECTIVES

To determine the clinical efficacy of the HIV-1 protease inhibitor indinavir (IDV) in saquinavir (SQV)-experienced patients and delineate the developing drug-resistance patterns.

DESIGN

Open-label prospective clinical trial.

SETTING

University hospital research center.

PATIENTS

Ten patients who had completed a SQV monotherapy study in which they had received SQV at a dose of 3600 or 7200 mg daily (two and fourfold the standard dose).

INTERVENTIONS

At enrollment patients received IDV for 4 weeks as monotherapy, after which zidovudine (ZDV) and lamivudine (3TC) were added to their drug regimen. Patients then received combination therapy (IDV-ZDV-3TC) for an additional 20 weeks to complete a total of 24 weeks of therapy.

MAIN OUTCOME MEASURES

Plasma HIV RNA viral load and CD4+ T-cell counts were monitored. Sequencing of the HIV protease gene was performed to determine the development of resistance mutations. Plasma samples for sequencing were taken before initial SQV therapy, after SQV therapy before starting IDV, and after 24 weeks of IDV therapy.

RESULTS

The average duration of high-dose SQV before starting IDV was 58+/-29.2 weeks. A 0.58 log10 RNA copies/ml increase was noted during the 3-week washout phase followed by a mean reduction in plasma HIV RNA viral load of 1.2 log10 RNA copies/ml after 4 weeks of IDV. After the addition of ZDV and 3TC at week 4, HIV RNA continued to fall reaching a mean reduction of 1.96 log10 RNA copies/ml at week 24. Plasma HIV RNA was below 400 RNA copies/ml in six out of nine patients at week 24. CD4+ T-cell counts showed a gradual rise from 328 x 10(6)/l to 453 x 10(6)/l by week 24. SQV therapy had resulted in multiple mutations in the protease gene. Six of the patients had developed five or more mutations: L90M in two, G48V in four (of which three also contained L101), and V82A in three. Patients in whom plasma HIV RNA was not durably suppressed by subsequent IDV combination therapy developed multiple (up to four) additional mutations within 24 weeks, including codons 54, 82 and 93 amongst others. No clear correlation was found between the mutations that had developed in individual patients after SQV and the subsequent efficacy of IDV.

CONCLUSION

Prolonged use of SQV at potent doses in the presence of elevated viral load levels resulted in the development of multiple resistance mutations. Individual resistance patterns varied greatly between patients, as did their virological response to therapy. Resistance assays may be useful in identifying which patients will benefit from salvage therapy with a second protease inhibitor.

Primary subtype C HIV-1 infection in Harare, Zimbabwe

Heterosexual transmission of HIV-1 is widespread in Southern Africa. Heteroduplex mobility assays (HMA) and phylogenetic analyses of V3-V5 envelope (env) gene sequences demonstrate that subtype C predominates in Zimbabwe. To elucidate factors contributing to the epidemic in Zimbabwe, clinical and virologic characteristics of recently acquired subtype C HIV-1 infection among 21 men and 1 woman were determined. In 12 of 19 men providing clinical histories, a sexually transmitted infection preceded serologic evidence of HIV-1, and 14 of 19 men complained of rash or fever before seroconversion. Quantitative p24 antigen levels, reverse transcriptase activity, and HIV RNA levels of 22 viral isolates correlated with in vitro infectivity in peripheral blood mononuclear cells (p < .05). Biologic phenotype assessed in MT-2 cells demonstrated that 3 of 22 isolates (14%) were syncytia inducing (SI) and the remaining 19 nonsyncytium inducing (NSI). Early growth of virus in culture was associated with increased plasma HIV RNA levels, decreased CD4 cell levels, and SI virus. Recent subtype C HIV-1 infection through heterosexual transmission in Zimbabwe demonstrated clinical and virologic features consistent with reports of seroconversion to subtype B viruses.

Role of preimmunization virus sequences in cellular immunity in HIV-infected patients during HIV type 1 MN recombinant gp160 immunization

The effect of patient preimmunization virus sequences on CTL responses during gp160 immunization were studied. Ten HLA-A2+, HIV+ asymptomatic patients with CD4+ T cells >500/mm3 were given two courses of HIV-1 MN rgp160 vaccine over a 2-year period. Envelope epitope-specific CTL responses, using PBMCs, were measured against peptide-coated autologous B lymphoblastoid cell lines. Optimum CTL epitopes were determined by HLA-A2-binding affinity of 9- to 10-mer peptides containing the HLA-A2.1-binding motif. Ten of the high- or intermediate-binding peptides were conserved among >50% of reported clade B HIV strains. These peptide-specific CTL activities and the patient virus sequences in peptide-coding regions were monitored. Six patients showed envelope peptide-specific CTL responses, which correlated with the presence of whole envelope antigen-specific CTL responses. Five of these patients, who showed responses to epitopes in the gp41 region (aa 814-824), had preimmunization virus similar to the vaccine sequence in this region. Three patients who did not show these epitope-specific responses had initially different sequences in the HIV gene encoding that region. The epitope-specific CTL responses appear to reflect recall responses, as only patients infected with virus containing the vaccine sequence developed them and they could be recalled with a second set of vaccine injections. This appears to be reminiscent of the concept of T cell "original antigenic sin." This vaccine was also immunogenic as measured by gp160-specific lymphocyte-proliferative responses. However, increased immune responses did not impact the HIV load or CTL epitope sequences during therapy.

Quantitation of HIV-1 RNA viral load using nucleic acid sequence based amplification methodology and comparison with other surrogate markers for disease progression

In this study, HIV-1 viral blood quantitation determined by Nucleic Acid Sequence Based Amplification (NASBA) was compared with other surrogate disease progression markers (antigen p24, CD4/CD8 cell counts and beta-2 microglobulin) in 540 patients followed up at São Paulo, SP, Brazil. HIV-1 RNA detection was statistically associated with the presence of antigen p24, but the viral RNA was also detected in 68% of the antigen p24 negative samples, confirming that NASBA is much more sensitive than the determination of antigen p24. Regarding other surrogate markers, no statistically significant association with the detection of viral RNA was found. The reproducibility of this viral load assay was assessed by 14 runs of the same sample, using different reagents batches. Viral load values in this sample ranged from 5.83 to 6.27 log (CV = 36%), less than the range (0.5 log) established to the determination of significant viral load changes.

Changes in CD4+ and CD8+ T cell subsets in response to highly active antiretroviral therapy in HIV type 1-infected patients with prior protease inhibitor experience

This study explores whether previous failures on antiretroviral drug regimens preclude the possibility of immune restoration. This was assessed by evaluating T cell subset changes in individuals who received a salvage regimen of highly active antiretroviral therapy (HAART) after initially failing protease inhibitor monotherapy. Ten HIV-1-infected asymptomatic patients received a regimen of indinavir, zidovudine, and 3TC after failing saquinavir monotherapy. Changes in absolute numbers of naive, memory, and activated CD4+ and CD8+ T cells expressing a selection of CD45RA, CD62L, CD45RO, HLA-DR, and CD38 markers were monitored prospectively over 6 months. These measurements were correlated with plasma viral load along with alterations in a selected CD8+ V alpha/Vbeta T cell receptor (TCR) repertoire. Over 6 months there was a progressive increase in numbers of CD4+ memory (CD45RA-CD62L+) and naive (CD45RA+CD62L+) T cells, which displayed a modest inverse correlation with viral load. Two phases of CD8+ memory cell changes were identified, consisting of a transient increase in CD45RA+CD62L- numbers after 2 months and thereafter a progressive rise in CD45RA-CD62L+ cells until 6 months. A strong correlation existed between reduced viral load and loss of activated CD8+CD38+HLA-DR+ cell numbers. There was also a temporary broadening of the CD8+ V alpha/Vbeta TCR repertoire at 8 weeks, which became skewed after 6 months in parallel with reduced viral suppression. Closer analysis of naive and memory cell subset proportions in individual patients revealed that enlarged pools of naive subsets were evident in those patients with rebounds in viral load. Overall, drug-experienced patients responding to HAART displayed increased numbers of naive and memory CD4+ subsets, and reduced CD8+ cell activation with a loss of TCR skewing.

A pilot clinical trial of HIV antigen-pulsed allogeneic and autologous dendritic cell therapy in HIV-infected patients

A pilot study was carried out to assess the safety and antigen-presenting properties of allogeneic or autologous dendritic cells (DCs) in six HLA-A2+, HIV-infected patients. Allogeneic DCs obtained from the peripheral blood of HLA-identical, HIV-seronegative siblings were pulsed with recombinant HIV-1 MN gp160 or synthetic peptides corresponding to HLA-A2-restricted cytotoxic epitopes of envelope, Gag, and Pol proteins. The antigen-pulsed cells were infused intravenously six to nine times at monthly intervals and HIV-specific immune responses were monitored. One allogeneic DC recipient with a CD4+ T cell count of 460/mm3 showed increases in envelope-specific CTL- and lymphocyte-proliferative responses, as well as in IFN-gamma and IL-2 production. Another allogeneic DC recipient with a CD4+ T cell count of 434/mm3 also showed an increase in HIV envelope-specific lymphocyte-proliferative responses. A recipient of autologous DCs with a CD4+ T cell count of 730/mm3 showed an increase in peptide-specific lymphocyte-proliferative responses after three infusions. Three other allogeneic DC recipients with CD4+ T cell counts <410/mm3 did not show increases in their HIV-specific immune responses. No clinically significant adverse effects were noted in this study and CD4+ T cell numbers and plasma HIV-1 RNA detected by RT-PCR of all six patients were stable during the study period. Thus, both allogeneic and autologous DC infusions were well tolerated and in patients with normal or near normal CD4+ T cell counts administration of these antigen-pulsed cells enhanced the immune response to HIV. However, since no effect on viral load was observed there was no evidence that this approach provided clinical benefit.

Optimization of specimen-handling procedures for accurate quantitation of levels of human immunodeficiency virus RNA in plasma by reverse transcriptase PCR

Human immunodeficiency virus type 1 (HIV-1) RNA levels in plasma are currently widely used clinically for prognostication and in monitoring antiretroviral therapy. Accurate and reproducible results are critical for patient management. To determine the effects of specimen collection and handling procedures on quantitative measurement of HIV-1 RNA, we compared anticoagulants and sample processing times. Whole blood was collected from 20 HIV-1-infected patients in EDTA, acid citrate dextrose (ACD), and heparin tubes, aliquoted, and stored at room temperature. Plasma was separated from whole-blood aliquots prepared at < or =1, 3, 6, 24, and 48 h postcollection and then stored at -70 degrees C until use. HIV-1 RNA levels were determined by the AMPLICOR HIV-1 MONITOR assay. Heparinized plasma samples, which were pretreated with heparinase prior to analysis, had the lowest baseline HIV-1 RNA levels. In the first 6 h, HIV-1 RNA levels decreased by 10, 20, and 31% in EDTA, ACD, and heparin tubes, respectively. From 6 to 48 h postcollection, HIV-1 RNA levels decreased in all anticoagulants, albeit at a slower, more consistent rate. Our results indicate that EDTA should be the anticoagulant of choice for plasma HIV-1 RNA measurement by reverse transcriptase PCR, but ACD tubes are acceptable if the plasma is separated within 6 h of blood collection. Caution must be applied in the interpretation of absolute HIV-1 RNA copy number values obtained with suboptimal specimen collection and processing procedures.

Stability of human immunodeficiency virus RNA in blood specimens as measured by a commercial PCR-based assay

We investigated the effects of conditions often encountered during handling, transit, and storage of blood specimens on the quantity of detectable human immunodeficiency virus (HIV) RNA in plasma. HIV RNA copy numbers were measured with a commercially available assay (the Amplicor HIV-1 Monitor test kit). Variables examined were the time to processing of blood and plasma, the holding temperature of blood and plasma prior to processing, the effect of freezing and thawing of plasma, and the use of different anticoagulants. The relationship between the HIV RNA copy number and the HIV isolation rate by peripheral blood mononuclear cell (PBMC) coculture was also examined. We found that RNA copy numbers were maintained to within 0.5 log10 (approximately threefold) in blood and plasma samples held at room temperature or 4 degrees C for up to 3 days and remained stable despite (limited) freezing and thawing of the plasma. HIV RNA copy numbers were also maintained after long-term storage of plasma at -70 degrees C. The ability to isolate HIV from PBMCs was directly proportional to the HIV RNA copy number.

Comparison of the Amplicor HIV-1 monitor test and the nucleic acid sequence-based amplification assay for quantitation of human immunodeficiency virus RNA in plasma, serum, and plasma subjected to freeze-thaw cycles

The Amplicor HIV-1 Monitor test was compared to the nucleic acid sequence-based amplification (Nasba) assay system for the quantitation of human immunodeficiency virus (HIV) RNA in three different types of clinical samples: plasma, serum, and plasma subjected to freeze-and-thaw cycles. Each assay detected HIV RNA in the same 73 (90%) of 81 samples tested, and the quantitative results obtained with the two assays were significantly correlated. Both assays detected higher RNA levels in patients with CD4+ cell counts lower than 200 cells/mm3 than in patients with CD4+ cell counts higher than 200 cells/mm3. In addition, RNA levels in plasma higher than 5 logs predicted higher numbers of clinical events than did RNA levels in plasma lower than 5 logs. Quantitation of HIV RNA in paired plasma and serum samples showed lower HIV RNA content in serum than in the paired plasma sample, with mean differences between HIV RNA contents of plasma and serum of 0.54 and 0.28 log RNA copy/ml by the Nasba assay and the Amplicor HIV-1 Monitor assay, respectively. No significant loss of HIV RNA was detected with either assay in plasma samples subjected to multiple freeze-and-thaw cycles. These studies demonstrate that the Nasba and Amplicor assays perform similarly with plasma and serum samples. Further, the results indicate that freeze-and-thaw cycles do not result in significant loss of detectable HIV RNA.

Stability of HIV-1 RNA in blood during specimen handling and storage prior to amplification by NASBA-QT

The influence of different storage temperatures and anticoagulation conditions on the HIV-1 RNA load as measured by NASBA-QT was examined. Blood specimens from 14 HIV-1 infected individuals were processed within 2 h after collection. The HIV-1 RNA load remained stable for at least 6 months when samples were frozen directly at -70 degrees C in lysis buffer. This lysis buffer fully inactivated the virus. When whole EDTA blood was stored, the HIV-1 RNA load was stable for 72 h at 25 degrees C, but it declined within 24 h at 4 degrees C. The HIV-1 RNA load in whole heparinized blood declined significantly after 24 h at both 4 and 25 degrees C. It was slightly lower (average of 0.18 log ml-1) than in whole EDTA blood. At 4 degrees C, the HIV-RNA load in serum and EDTA-plasma stored with lysis buffer did not decline up to 14 days. At + 30 degrees C, however, the load declined significantly after 2 days. Of clinical significance, the mean load in EDTA plasma was 0.5 log ml-1 higher than in serum. This difference was patient dependent (range 0.1-0.7 log ml-1). We thus recommend, for quantifying HIV-1 RNA by NASBA, to use preferably EDTA blood which is kept at room temperature until plasma separation. When using heparinized blood, the plasma should be stored frozen within 8 h.

Effect of therapeutic immunization with recombinant gp160 HIV-1 vaccine on HIV-1 proviral DNA and plasma RNA: relationship to cellular immune responses

Therapeutic vaccination has been proposed as a strategy to augment immune mechanisms to control viral replication and slow clinical progression of HIV infection to disease. Following recombinant gp160 (r-gp160) immunization in three clinical trials, plasma HIV-1 RNA and cellular proviral DNA were assessed by quantitative polymerase chain reaction (PCR) in 76 HIV-seropositive subjects with CD4+ T cell counts > or = 300/mm3. Immunization increased HIV-specific cellular immune responses (e.g., cytotoxic T lymphocyte [CTL] activities, lymphocyte proliferative responses); however, there were no significant effects of immunization or cellular immune responses on measures of plasma RNA or cellular DNA viral load.

Human immunodeficiency virus type 1 reverse transcriptase genotype and drug susceptibility changes in infected individuals receiving dideoxyinosine monotherapy for 1 to 2 years

The genetic mechanisms of human immunodeficiency virus type 1 (HIV-1) resistance to dideoxyinosine (ddI) in vivo have been described based on data from primary HIV-1 isolates. To better define the spectrum of HIV-1 reverse transcriptase (RT) changes occurring during ddI therapy, we determined the genotype and ddI susceptibility of the RT gene of HIV RNA isolated from the plasma of 23 patients who had received 1 to 2 years (mean, 87 +/- 16 weeks) of ddI monotherapy. Population-based sequencing of plasma virus showed that 12 of 23 (52%) patients developed known ddI resistance mutations: L74V (7 patients), K65R (2 patients), L74V with M184V (3 patients), and L74V with K65R (1 patient). Five patients developed one or more known zidovudine resistance mutations (at codons 41, 67, 70, 215, and/or 219) during the study. Other amino acid substitutions were found, but only S68G and L210W occurred in more than one patient. Studies of sensitivity to ddI were performed on population-based recombinant-virus stocks generated by homologous recombination between a plasmid containing an HXB2 clone with the RT gene deleted and RT-PCR products of the RT genes from patients' plasma RNA. The sequences of the virus stocks produced by this procedure were typically identical to the sequence of the input PCR product from plasma RNA. Both an MT-2 cell-based culture assay and a cell-free virion-associated RT inhibition assay showed that viruses possessing an L74V and/or M184V mutation or a K65R mutation had reduced sensitivity to ddI. Viruses without these specific mutations had no change in sensitivity to ddI. The results presented here show that the spectrum of RT mutations in a population of patients on ddI monotherapy is more complex than previously described. The development of multiple mutational patterns, including those that confer resistance to other nucleoside analogs, highlights the complexity of using the currently available nucleoside analogs for antiretroviral therapy.

The effect of maternal viral load on the risk of perinatal transmission of HIV-1. New York City Perinatal HIV Transmission Collaborative Study Group

OBJECTIVE

To determine the effect of maternal viral load at delivery on the risk of perinatal transmission of HIV-1.

DESIGN

A nested case-control study within a prospectively followed cohort of HIV-1-infected pregnant women and their infants.

SETTING

The multicenter New York City Perinatal HIV Transmission Collaborative Study.

PARTICIPANTS

Fifty-one women who gave birth to HIV-1 infected infants were frequency-matched within CD4+ cell count quintiles with 54 non-transmitting mothers.

MAIN OUTCOME MEASURES

Maternal quantity of HIV-1 viral RNA was assayed in plasma obtained near delivery using the nucleic acid sequence-based amplification assay system.

RESULTS

Viral RNA was detected in 73 (70%) out of 105 women and the median viral load was 16,000 RNA copies/ml in transmitters and 6,600 in non-transmitters (P < 0.01). When adjusted for maternal CD4+ count near delivery, women with measurable viral load were nearly sixfold more likely to transmit HIV-1 than women with viral load below detection [adjusted odds ratio (AOR), 5.8; 95% confidence interval (CI), 2.2 15.5]. The odds ratio for perinatal transmission of log10 viral load, adjusted for CD4 count was 2.7 (95% CI, 1.5-5.1). When stratified by the stage of HIV-1 disease, the only group with significant association between log10 viral load and transmission were AIDS-free women with CD4+ count > 500 x 10(6)/l (AOR, 9.1; 95% CI, 2.6-31.5).

CONCLUSIONS

High maternal viral load increases the likelihood of perinatal transmission of HIV-1 in women without AIDS and advanced immunosuppression. HIV-1 infected pregnant women without advanced disease, shown by others to have the lowest risk of perinatal transmission, may benefit the most from efforts to identify and decrease viral load at delivery.

Comparison of QIAamp HCV kit spin columns, silica beads, and phenol-chloroform for recovering human immunodeficiency virus type 1 RNA from plasma

Human immunodeficiency virus type 1 (HIV-1) pol mutations are responsible for HIV-1 resistance to current antiretroviral drugs. HIV-1 RNA extraction with QIAamp HCV kit spin columns (Qiagen, Chatsworth, Calif.) followed by reverse transcription-PCR successfully recovered a 1,008-bp pol fragment from the plasma of 31 of 34 HIV-1-infected patients that was suitable for sequencing and recombinant-virus studies. The minimum HIV-1 RNA concentration required for gene recovery was 30 to 40 copies/ml, which was similar to the minimal HIV-1 RNA concentration required when phenol-chloroform or silica beads are used for RNA extraction.

Plasma viremia in macaques infected with simian immunodeficiency virus: plasma viral load early in infection predicts survival

A reliable method for the quantitation of plasma viremia in nonhuman primates infected with simian immunodeficiency virus (SIV) and related viruses is described. This method is based on an established quantitative-competitive PCR format and includes a truncated control for internal assay calibration. Optimization of assay conditions has significantly improved amplification specificity, and interassay variability is comparable to that of commercially available assays for human immunodeficiency virus (HIV) quantitation. This procedure was used to monitor viral loads in a group of Macaca mulatta animals that were infected with SIVsmE660 for over 2 years. Highly diverse profiles of plasma viremia were observed among animals, and high viral loads were associated with more rapid disease progression. Spearman rank correlation analyses were done for survival versus three parameters of viral load: plasma viremia, p27 core antigen, and frequency of infected peripheral blood mononuclear cells. Plasma viremia had the strongest overall correlation and was significantly (P < 0.05 to P < 0.01) associated with survival at 10 of the 13 time points examined. Plasma viremia did not correlate with survival during the primary viremia phase; however, the strength of this correlation increased with time postinfection and, remarkably, viremia levels as early as week 6 postinfection were highly predictive (P < 0.01) of relative survival. These findings are consistent with the available clinical data concerning viral load correlates early in HIV infection, and they provide further support for the view that disease outcome in lentiviral infection may be largely determined by events that occur shortly after infection.

Comparative evaluation of three assays for the quantitation of human immunodeficiency virus type 1 RNA in plasma

Reverse transcriptase-coupled polymerase chain reaction (Amplicor HIV-1 Monitor), the branched DNA (bDNA) method (Quantiplex HIV-1 RNA) and the nucleic acid sequence-based assay (NASBA HIV-1 RNA QT) were comparatively evaluated for the quantitation of human immunodeficiency virus type 1 (HIV-1) RNA in plasma. Among 60 plasma specimens from HIV-1 infected patients, HIV-1 RNA was detected in 56 by Amplicor (sensitivity, 93.3%), in 41 by bDNA (sensitivity, 68.3%), and in 60 by NASBA (sensitivity, 100%). HIV-1 RNA was not detected by any of these methods in 34/34 plasma specimens from HIV-1-seronegative blood donors (specificity, 100%). The HIV-1 RNA levels as determined by the different methods were correlated significantly. The frequency of concordant results (log difference < 0.50) was 80.4% between Amplicor and NASBA, 77.5% between Amplicor and bDNA, and 58.6% between bDNA and NASBA. After initiation of antiviral therapy, HIV-1 RNA level variations observed with the three methods were similar. HIV-1 RNA levels were inversely correlated with the CD4+ T cell counts, whereas no correlation was found with HIV-1 p24-antigen levels. When the methods were evaluated for reproducibility, coefficients of variation ranged from 11% to 40% for Amplicor, from 6% to 35% for bDNA, and from 13% to 62% for NASBA. Quantitation of HIV-1 RNA in culture supernatants from HIV-1 subtype A to H strains showed that bDNA can be used to quantitate RNA from all HIV-1 subtypes, whereas Amplicor failed to detect RNA from subtype A strains and NASBA subtype G strains.

Evaluation of a quality assurance program for quantitation of human immunodeficiency virus type 1 RNA in plasma by the AIDS Clinical Trials Group virology laboratories

A number of quantitative assays have been developed by using amplification techniques to measure human immunodeficiency virus type 1 RNA in the plasma of infected individuals. The Virology Committee of the AIDS Clinical Trials Group in the Division of AIDS, National Institute of Allergy and Infectious Diseases, has established a quality assurance program (QAP) for quantitative assays of HIV-1 RNA levels in plasma. The primary objective of the QAP was to ascertain that a laboratory could maintain the precision required to have a 90% power to detect a fivefold difference in RNA copy number between two samples in the same batch. To achieve this goal, the QAP required an intra-assay standard deviation of no greater than 0.15 log10 RNA copies per ml. Panels for proficiency testing consisted of coded replicate samples and a common set of standards. To date, 41 laboratories have participated in the program and have used both commercial and in-house assays. We demonstrated that 65% of the laboratories were capable of attaining the necessary level of intra-assay precision. The fitted regressions indicated that the differences among laboratories that used the same kit were generally greater than the differences among population-average regressions for the kits themselves. The use of an external QAP and a common set of standards reduced differences both among laboratories that used the same kit and among laboratories that used different kits. Thus, use of a common set of standards across clinical trial protocols would allow for cross-protocol comparisons.

Nevirapine-resistant human immunodeficiency virus: kinetics of replication and estimated prevalence in untreated patients

The nonnucleoside reverse transcriptase inhibitor nevirapine rapidly selects for mutant human immunodeficiency virus (HIV) in vivo. The most common mutation occurs at amino acid residue 181 in patients receiving monotherapy. After the initiation of nevirapine therapy, plasma and peripheral blood mononuclear cell samples were collected at frequent intervals and assayed for HIV RNA levels and the proportion of virus containing a mutation at residue 181. HIV RNA levels remained stable for the first 24 h after initiation of therapy and rapidly declined between 1 and 7 days. There was a consistent maximum decrease of 2 log10 HIV RNA copies per ml of plasma (range, 1.96 to 2.43) from baseline after 2 weeks in all monotherapy subjects. The estimated median half-life of HIV RNA was 1.11 days (range, 0.63 to 1.61). After 14 days of therapy, HIV RNA levels began to increase and 181 mutant virus was detected. The estimated doubling time of the emerging virus population ranged from 1.80 to 5.73 days. Viral DNA in peripheral blood mononuclear cells turned over from wild type to the mutant with a mutation at residue 181 significantly more slowly than did HIV RNA in plasma. In two subjects, the calculated prevalence of the 181 mutant virus prior to treatment was 7 and 133 per 10,000 copies of plasma HIV RNA.

Isolation of HIV-1 RNA from plasma: evaluation of eight different extraction methods

The efficacy of eight different methods for the extraction of HIV-1 RNA from plasma was compared. The RNA preparation method that gave the best results by RT-PCR was the one described by Chomczynski and Sacchi (1987, Anal. Biochem. 162, 156-159). This method consists of a guanidine thiocyanate treatment followed by three phenol-chloroform-isoamylalcohol extractions and an ethanol precipitation. The disadvantage of this method is that it is time consuming and less suitable for the extraction of large series of samples. Moreover, due to the large number of procedural steps, there is a greater risk of sample mix-up or contamination. Of the single-step RNA purification methods, good results were obtained with the TRIzol method (Gibco Life Technologies, Paisley, UK) and with the extraction method offered by the NASBA kit (Organon Teknika, Turnhout, Belgium). The above single-step methods are recommended since both are sensitive enough to detect low copy numbers of HIV-RNA in the plasma of asymptomatic patients, and require only 2 h for completion. For most of the methods evaluated the inter-test variability was acceptable (mean variation coefficient between duplicate extraction varied between 17.3 and 47.3%). Inter-laboratory reproducibility was evaluated only for the TRIzol-method and found to be low (mean variation coefficient 63.4).

Assessment of a standardized reverse-transcriptase PCR assay for quantifying HIV-1 RNA in plasma and serum

The analytical variability of the new commercially available Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) assay, Amplicor HIV-1 Monitor, has been assessed to establish criteria for assessing the significance of HIV-1 RNA level measurements. Estimations of the standard deviations (SD) of log-copies in inter-assay (mean 0.09 log) and in inter-laboratory (mean 0.14 log) reproducibility experiments demonstrated that the assay can discriminate with 95% confidence between 3-fold (inter-assay) and 5-fold differences (inter-laboratory). The inter-lot reproducibility (mean 0.10 log) was similar to the inter-assay reproducibility. The HIV-1 RNA concentrations measured in plasma collected in potassium EDTA anticoagulant were slightly higher than those measured in plasma collected in sodium citrate. The HIV-1 RNA concentrations measured in sera were about 50% of the HIV-1 RNA concentrations measured in paired plasma samples. However, there was a strong correlation between these two measurements (P < 0.0001). The assay was used to measure viral RNA in the plasma of 50 HIV-1 positive individuals at different stages of infection. All the individuals had detectable HIV-1 RNA (300-957000 copies/ml). There was no correlation between HIV-1 RNA and Immune Complex Dissociated (ICD) p24 antigen, but HIV-1 RNA was correlated with CD4+ cell counts (P < 0.0001) and the clinical stage (P = 0.0042), with higher HIV-1 RNA concentrations in patients with a more advanced stage of the disease. The significant association of HIV-1 RNA with major markers of HIV infection and the reliability of this sensitive, easy-to-use RT-PCR assay indicate its suitability for use in clinical trials and suggest that this assay is appropriate for routine clinical applications.

Fluctuations in steady state level of genomic HIV-1 RNA and replication intermediates related to disease progression rate

Steady state levels of HIV-1 genomic RNA and unintegrated circular DNA fluctuate in the course of HIV-1 infection. Genomic RNA in serum was detected using the NASBA technique and the amount of circular DNA was assessed by PCR. Quantification was done by competitive techniques using co-amplification of internal standards. Within the Amsterdam Cohort Studies it was possible to distinguish rapid progressors, intermediate progressors, slow progressors and non-progressors. Rapid progressors show persistently high viral RNA loads from seroconversion on, while all other HIV-1-infected individuals show a steady decline after seroconversion. Subsequent rises in viral RNA levels herald disease progression in later stages of infection. Unintegrated circular DNA shows similar, but somewhat delayed kinetics. These results indicate that the distribution of AIDS and the average length of the symptom-free period in an HIV-1-infected host population is determined by the steady state levels of genomic RNA and of replication intermediates that are produced by a particular HIV-1 virus population in the average seropositive individual.

Comparative evaluation of NASBA HIV-1 RNA QT, AMPLICOR-HIV monitor, and QUANTIPLEX HIV RNA assay, three methods for quantification of human immunodeficiency virus type 1 RNA in plasma

Three commercial assays for quantifying plasma human immunodeficiency virus type 1 (HIV-1) RNA were evaluated. The assays differed in their sample volumes, the means of preparing samples, and methods of amplification and detection. Plasma samples were obtained from 36 HIV-1-infected patients representing all stages of HIV-1 infection and were analyzed as coded specimens. Measurement of HIV-1 RNA baseline levels revealed no significant difference in sensitivity between the three assays. The assays were also applied to the quantitation of HIV-1 RNA levels in the plasma of patients who were changing their antiretroviral therapy. The changes measured in HIV-1 RNA levels in plasma in response to therapy were comparable by the three assays. No close correlation was found between the amount of HIV-1 RNA and the CD4 T-cell count; HIV-1 RNA assays were more sensitive than p24 antigen assays as an indicator of plasma viremia. Overall, the study demonstrates that all three quantitative assays for HIV-1 RNA can be used to measure the HIV-1 RNA copy number representing the HIV-1 viremia status in patients with HIV-1 infection. Since this copy number is likely to be useful in monitoring the effectiveness of antiviral therapy, these quantitative assays for HIV-1 RNA are ready to be built into clinical trials.

Role of methionine 184 of human immunodeficiency virus type-1 reverse transcriptase in the polymerase function and fidelity of DNA synthesis

Methionine 184 of HIV-1 RT is a constituent of the catalytically crucial and highly conserved YXDD motif in the reverse transcriptase class of enzymes. We investigated the role of this residue by substituting it with Ala and Val by site-directed mutagenesis followed by extensive characterization of the two mutant enzymes. The kinetic parameters governing DNA synthesis directed by RNA and DNA templates indicated that both M184A and M184V mutants are catalytically as efficient as the wild type enzyme. Photoaffinity labeling of both the mutant and the wild type enzyme exhibited an identical affinity for RNA-DNA and DNA-DNA template primers. We further demonstrate that M-->V substitution at 184 position significantly increases the fidelity of DNA synthesis while M-->A substitution results in a highly error-prone enzyme without having compromised its efficiency of DNA synthesis. The M184V mutant exhibited a 25-45-fold increase in mismatch selectivity (ratio of k(cat)/K(m) of correct versus incorrect nucleotides) as compared to the WT enzyme. This pattern of error-prone synthesis is also confirmed by examining the abilities of the enzyme-(template-primer) covalent complexes to incorporate correct versus incorrect nucleotide onto the immobilized template-primer. The nature of error-prone synthesis by the M184A mutant shows an increase in both the mismatch synthesis and extension of the mismatched primer termini. Using a three-dimensional molecular model of the ternary complex of HIV-1 RT, template-primer, and dNTP, we observe that the strategic location of M184 may allow it to interact with the sugar moiety of either the primer nucleotide or the dNTP substrate.

Multidrug-resistant human immunodeficiency virus type 1 strains resulting from combination antiretroviral therapy

Multidrug-resistant human immunodeficiency virus type 1 (HIV-1) strains with reverse transcriptase (RT) mutations at codons A62-->V, V75-->I, F77-->L, F116-->Y, and Q151-->M have been reported in patients receiving combination therapy with zidovudine (AZT) and didanosine (ddI). Infectious clones with each mutation alone, all five mutations together, and various combinations of mutations were created by site-directed mutagenesis. Mutation Q151-->M conferred partial resistance to AZT, ddI, zalcitibine, and stavudine, whereas a combination of four mutations conferred increased resistance to AZT, ddI, zalcitibine, and stavudine. The positions of residues 75, 77, and 151 in the three-dimensional crystal structure of HIV-1 RT suggest that these residues may affect the ability of the enzyme to discriminate between deoxynucleoside triphosphates and nucleoside analog RT inhibitors. Replication experiments showed that clones with mutation F77-->L but without V75-->I (HIV-1(77), HIV-1(77,151), and HIV-1(77,116,151) had attenuated growth compared with that of the original HIV-1NL4-3 strain and strains containing mutations at both positions 75 and 77 (HIV-1(75,77,151) and HIV-1(75,77,116,15)). Sequence analysis of viral RNA and proviral DNA from several patients indicated that RT mutations developed in a sequential and cumulative pattern over the course of a 2- to 4-year observation period. The present results suggest that drug resistance and viral replicative capacity both may play a role in selection of HIV-1 RT mutations.

Application of a commercial kit for detection of PCR products to quantification of human immunodeficiency virus type 1 RNA and proviral DNA

Quantitative tests for human immunodeficiency virus type 1 (HIV-1) RNA in plasma and proviral DNA in peripheral blood mononuclear cells (PBMC) provide valuable information on the status of HIV-1 infection. This paper describes tests that were carried out with commercially available materials and an enzyme-linked immunosorbent assay reader for detecting spectrophotometric changes. Samples consisted of 100 microliters of plasma or 200,000 PBMC. The procedure involved sample preparation, PCR-based amplification with the primer pair SK39 (biotinylated at the 5' end) and SK38, hybridization of the cDNA PCR product to an RNA probe, capture of the RNA-DNA hybrid on a solid phase by means of strepavidin, binding to an alkaline phosphatase-conjugated antibody directed against RNA-DNA hybrids, and incubation with p-nitrophenylphosphate. Spectrophotometric changes were recorded at four intervals over a period of 20 h. The inclusion of HIV-1 RNA or proviral DNA standards in each run was an integral part of the procedure. The dynamic ranges afforded by these assays--500 to 1 million RNA copies per ml and 10 to 5,000 proviral DNA copies per 10(6) PBMC--were applicable to most plasma specimens and to all PBMC specimens from HIV-1-infected patients. Correlations of log-transformed HIV-1 RNA and proviral DNA concentrations with those found by reference methods were, respectively, 0.88 and 0.80. The between-run coefficients of variation for the detection method were < or = 25% (range, 9.1 to 24.7) and < or = 15% (range, 10.9 to 15.1), respectively, for HIV-1 RNA and proviral DNA. The reproducibility of the overall procedure for HIV-1 RNA in plasma (including sample preparation, amplification, and detection) was given by a duplicate standard deviation of log10 copies per ml of 0.11. Thus, the method was sufficiently precise to allow the detection of fourfold changes in plasma HIV-1 RNA concentrations, with a power of 0.95.

Kinetic analysis of intravirion reverse transcription in the blood plasma of human immunodeficiency virus type 1-infected individuals: direct assessment of resistance to reverse transcriptase inhibitors in vivo

Intravirion reverse transcripts have been identified in the blood plasma of human immunodeficiency virus type 1 (HIV-1)-infected individuals. In the present studies, the kinetic processes of intravirion HIV-1 reverse transcription, in the blood plasma of HIV-1-infected persons treated with nevirapine, were investigated. Nevirapine is a nonnucleoside inhibitor of reverse transcriptase (RT) which decreases the level of HIV-1 viral particles in the blood plasma of infected individuals. By analyzing HIV-1 virions at different time points prior to and after initiation of nevirapine therapy in vivo, the levels of intravirion reverse transcripts have been demonstrated to be dramatically susceptible to this anti-RT agent, out of proportion to effects on plasma virion load. The intravirion reverse transcripts were also documented to rebound to the pretreatment levels, concomitant with the development of resistant viral mutants. In addition, the infectivity of HIV-1 virions dramatically decreased after nevirapine treatment, further indicating that the effects of this anti-RT agent begin within the cell-free virions. Since the levels of intravirion reverse transcripts were altered according to the susceptibility or resistance of the HIV-1 RT enzyme to this inhibitor, these data demonstrate that the formation of intravirion reverse transcripts is a dynamic process in vivo. Moreover, because the alteration in ratios between intravirion HIV-1 reverse transcripts and viral genomic RNA directly reflects the efficiency of reverse transcription, we propose that the determination of these ratios in the blood plasma of HIV-1-positive patients may be a useful and, most importantly, a direct assay to monitor the efficacy of anti-RT agents in vivo.

Maternal plasma human immunodeficiency virus type 1 RNA level: a determinant and projected threshold for mother-to-child transmission

To prevent mother-to-child human immunodeficiency virus type 1 (HIV-1) transmission, it is important to identify its determinants. Because HIV-1 RNA levels can be reduced by antiviral therapy, we examined the role of maternal plasma HIV-1 RNA level in mother-to-child transmission. We used quantitative competitive PCR to measure HIV-RNA in 30 infected pregnant women and then followed their infants prospectively; 27% of the women transmitted HIV-1 to their infants and maternal plasma HIV-1 RNA level correlated strikingly with transmission. Eight of the 10 women with the highest HIV-1 RNA levels at delivery (190,400-1,664,100 copies per ml of plasma) transmitted, while none of the 20 women with lower levels (500-155,800 copies per ml) did (P = 0.0002). Statistical analysis of the distribution of HIV-1 RNA loads in these 30 women projected a threshold for mother-to-child transmission in a larger population; the probability of a woman with a viral RNA level of < or = 100,000 copies per ml not transmitting is predicted to be 97%. Examination of serial HIV-1 RNA levels during pregnancy showed that viral load was stable in women who did not initiate or change antiviral therapy. These data identify maternal plasma HIV-1-RNA level as a major determinant of mother-to-child transmission and suggest that quantitation of HIV-1 RNA may predict the risk of transmission.

Distinct changes in HIV type 1 RNA versus p24 antigen levels in serum during short-term zidovudine therapy in asymptomatic individuals with and without progression to AIDS

Serum HIV-1 RNA and p24 antigen levels were examined in 28 seropositive asymptomatic individuals participating in a trial on the efficacy of zidovudine. Sixteen individuals remained asymptomatic until 4 years after the onset of the trial, whereas 12 individuals were diagnosed with an AIDS-defining event. The serum HIV-1 RNA load and p24 antigen levels were determined before the onset of therapy and during the first 8 weeks of therapy to establish whether the patterns of change were predictive of clinical outcome. Among the 28 participants 43% had measurable pretreatment concentrations of p24 antigen. Initiation of zidovudine therapy was followed by a similar decline of p24 antigen levels in nonprogressors as well as progressors and, therefore, these groups could not be distinguished on the basis of this parameter. HIV-1 RNA was detected in the pretreatment samples of 82% of the individuals and could be detected in p24 antigen-positive as well as p24 antigen-negative individuals. Similar changes in HIV-1 RNA load during zidovudine therapy were observed in p24 antigen-positive and -negative individuals. Analysis of the HIV-1 RNA response according to clinical outcome demonstrated that HIV-1 RNA copy numbers had declined significantly after 4 weeks of therapy in both nonprogressors and progressors, but the decline in RNA load was much stronger in the nonprogressors. Our data show that the HIV-1 RNA load in serum can be used to monitor the response to antiviral therapy in p24 antigen-positive as well as -negative individuals. Posttreatment changes in p24 antigen levels are not indicative for clinical outcome, whereas RNA copy numbers are.(ABSTRACT TRUNCATED AT 250 WORDS)

Clinical evaluation of branched DNA signal amplification for quantifying HIV type 1 in human plasma

Quantification of HIV-1 RNA in human plasma has provided unique insight into AIDS pathogenesis and promises to hasten progress in antiretroviral therapy and vaccine research. However, no generally available HIV-1 RNA assay has yet been subjected to rigorous clinical testing or to comparative evaluation with research-based RNA assays using large numbers of well-characterized clinical specimens. In this study, the Chiron Quantiplex branched DNA (bDNA) signal amplification assay was used to measure viral RNA in the plasma of 152 HIV-1-positive individuals at all stages of infection and in 12 patients before and after initiating zidovudine therapy. Eighty-six percent of patients had bDNA assay results above the 10,000-RNA Eq/ml sensitivity cutoff. Branched DNA values were significantly correlated with plasma viral RNA levels determined by quantitative competitive polymerase chain reaction (QC-PCR) assay (Spearman rank correlation, r = 0.89), infectious plasma virus titers (r = 0.72), p24 antigen levels (r = 0.51), immune complex dissociated p24 antigen levels (r = 0.56), and CD4+ lymphocyte counts (r = -0.72; p < 0.0001 for all comparisons). Plasma viral RNA determinations by bDNA and QC-PCR assays were quantitatively similar in the range of 10(4) to 10(7) RNA molecules/ml [log bDNA = 0.93 + 0.80 (log QC-PCR); R2 = 0.81, p < 0.0001] and declined identically following the institution of zidovudine therapy (68-73% decrease from baseline). The close quantitative correlation between bDNA and QC-PCR results, and their significant association with other viral markers and CD4+ counts, support the use of plasma viral RNA measurement in HIV-1 clinical trials.

Viral dynamics in human immunodeficiency virus type 1 infection

The dynamics of HIV-1 replication in vivo are largely unknown yet they are critical to our understanding of disease pathogenesis. Experimental drugs that are potent inhibitors of viral replication can be used to show that the composite lifespan of plasma virus and virus-producing cells is remarkably short (half-life approximately 2 days). Almost complete replacement of wild-type virus in plasma by drug-resistant variants occurs after fourteen days, indicating that HIV-1 viraemia is sustained primarily by a dynamic process involving continuous rounds of de novo virus infection and replication and rapid cell turnover.

Intravirion reverse transcripts in the peripheral blood plasma on human immunodeficiency virus type 1-infected individuals

Variable levels of viral DNA have been demonstrated within human immunodeficiency virus type 1 (HIV-1) virions purified from cell cultures. In the present studies, it is demonstrated that DNase-resistant viral DNA is associated with HIV-1 virions purified from the peripheral blood plasma of both symptomatic and asymptomatic HIV-1-infected individuals. The differences in viral DNA copy numbers, detected by quantitative PCR in various regions of the HIV-1 genome, indicated that the intravirion HIV-1 DNA is frequently, but perhaps not totally, the result of partial reverse transcription. These in vivo data suggest that it may be valuable to further investigate the impact of virion-associated viral DNA upon the efficiency of intra- and interhost HIV-1 transmission modes.

Quantification of human immunodeficiency virus in plasma by RNA PCR, viral culture, and p24 antigen detection

A semiquantitative PCR technique for detecting human immunodeficiency virus type 1 (HIV-1) RNA in plasma was compared with quantitative viral culture and p24 antigen detection in plasma. Ninety-three samples from 20 symptomatic, 10 asymptomatic, and 10 seronegative individuals were tested. For most of the seropositive patients, consecutives samples were examined. Viral RNA was extracted from plasma by the method described by Boom et al. (R. Boom, C.J. A. Sol, M. M. M. Salimans, C.L. Jansen, P. M. E. Wertheim-van Dillen, and J. van der Noordaa, J. Clin. Microbiol. 28:495-503, 1990). The RNA PCR was the most sensitive method (100 and 74% sensitivity for symptomatic and asymptomatic patients, respectively) and produced less divergent results with the consecutive samples from individual patients compared with the other techniques. All samples positive by viral culture or p24 antigen assay were also positive in the RNA PCR. For each of the three assays, the number of positive results obtained correlated with the disease stage. The estimated mean number of HIV-1 RNA copies was significantly higher in symptomatic patients (22,750 copies per ml) than in asymptomatic patients (1,820 copies per ml). It was also higher in samples positive for viral culture than in culture-negative samples. No close correlation was found between the amount of HIV-1 RNA and the amount of p24 antigen or the titer of infectious virus in plasma or between this titer and the level of p24 antigen. The plasma RNA PCR may be a useful additional marker of disease progression and may be valuable for monitoring the effects of antiviral therapy.